dcGOR 1.0.5

Function to conduct ontology enrichment analysis given a group of domains

Description

dcEnrichment is supposed to conduct enrichment analysis for an input group of domains using a specified ontology. It returns an object of S4 class "Eoutput". Enrichment analysis is based on either Fisher's exact test or Hypergeometric test. The test can respect the hierarchy of the ontology. The user can customise the background domains; otherwise, the function will use all annotatable domains as the test background

Usage

dcEnrichment(data, background = NULL, domain = c(NA, "SCOP.sf", "SCOP.fa", "Pfam", 
  "InterPro", "Rfam"), ontology = c(NA, "GOBP", "GOMF", "GOCC", "DO", "HPPA", "HPMI", 
      "HPON", "MP", "EC", "KW", "UP"), sizeRange = c(10, 1000), min.overlap = 3, which_distance = NULL, 
      test = c("HypergeoTest", "FisherTest", "BinomialTest"), p.adjust.method = c("BH", 
          "BY", "bonferroni", "holm", "hochberg", "hommel"), ontology.algorithm = c("none", 
          "pc", "elim", "lea"), elim.pvalue = 0.01, lea.depth = 2, verbose = T, domain.RData = NULL, 
      ontology.RData = NULL, annotations.RData = NULL, RData.location = "http://dcgor.r-forge.r-project.org/data")

Arguments

data
an input vector. It contains id for a list of domains, for example, sunids for SCOP domains
background
a background vector. It contains id for a list of background domains, for example, sunids for SCOP domains. If NULL, by default all annotatable domains are used as background
domain
the domain identity. It can be one of 'SCOP.sf' for SCOP superfamilies, 'SCOP.fa' for SCOP families, 'Pfam' for Pfam domains, 'InterPro' for InterPro domains, 'Rfam' for Rfam RNA families
ontology
the ontology identity. It can be "GOBP" for Gene Ontology Biological Process, "GOMF" for Gene Ontology Molecular Function, "GOCC" for Gene Ontology Cellular Component, "DO" for Disease Ontology, "HPPA" for Human Phenotype Phenotypic Abnormality, "HPMI" for Human Phenotype Mode of Inheritance, "HPON" for Human Phenotype ONset and clinical course, "MP" for Mammalian Phenotype, "EC" for Enzyme Commission, "KW" for UniProtKB KeyWords, "UP" for UniProtKB UniPathway. For details on the eligibility for pairs of input domain and ontology, please refer to the online Documentations at http://supfam.org/dcGOR/docs.html
sizeRange
the minimum and maximum size of members of each term in consideration. By default, it sets to a minimum of 10 but no more than 1000
min.overlap
the minimum number of overlaps. Only those terms that overlap with input data at least min.overlap (3 domains by default) will be processed
which_distance
which distance of terms in the ontology is used to restrict terms in consideration. By default, it sets to 'NULL' to consider all distances
test
the statistic test used. It can be "FisherTest" for using fisher's exact test, "HypergeoTest" for using hypergeometric test, or "BinomialTest" for using binomial test. Fisher's exact test is to test the independence between domain group (domains belonging to a group or not) and domain annotation (domains annotated by a term or not), and thus compare sampling to the left part of background (after sampling without replacement). Hypergeometric test is to sample at random (without replacement) from the background containing annotated and non-annotated domains, and thus compare sampling to background. Unlike hypergeometric test, binomial test is to sample at random (with replacement) from the background with the constant probability. In terms of the ease of finding the significance, they are in order: hypergeometric test > binomial test > fisher's exact test. In other words, in terms of the calculated p-value, hypergeometric test < binomial test < fisher's exact test
p.adjust.method
the method used to adjust p-values. It can be one of "BH", "BY", "bonferroni", "holm", "hochberg" and "hommel". The first two methods "BH" (widely used) and "BY" control the false discovery rate (FDR: the expected proportion of false discoveries amongst the rejected hypotheses); the last four methods "bonferroni", "holm", "hochberg" and "hommel" are designed to give strong control of the family-wise error rate (FWER). Notes: FDR is a less stringent condition than FWER
ontology.algorithm
the algorithm used to account for the hierarchy of the ontology. It can be one of "none", "pc", "elim" and "lea". For details, please see 'Note'
elim.pvalue
the parameter only used when "ontology.algorithm" is "elim". It is used to control how to declare a signficantly enriched term (and subsequently all domains in this term are eliminated from all its ancestors)
lea.depth
the parameter only used when "ontology.algorithm" is "lea". It is used to control how many maximum depth is uded to consider the children of a term (and subsequently all domains in these children term are eliminated from the use for the recalculation of the signifance at this term)
verbose
logical to indicate whether the messages will be displayed in the screen. By default, it sets to TRUE for display
domain.RData
a file name for RData-formatted file containing an object of S4 class 'InfoDataFrame' (i.g. domain). By default, it is NULL. It is only needed when the user wants to customise enrichment analysis using their own data. See dcBuildInfoDataFrame for how to creat this object
ontology.RData
a file name for RData-formatted file containing an object of S4 class 'Onto' (i.g. ontology). By default, it is NULL. It is only needed when the user wants to customise enrichment analysis using their own data. See dcBuildOnto for how to creat this object
annotations.RData
a file name for RData-formatted file containing an object of S4 class 'Anno' (i.g. annotations). By default, it is NULL. It is only needed when the user wants to customise enrichment analysis using their own data. See dcBuildAnno for how to creat this object
RData.location
the characters to tell the location of built-in RData files. By default, it remotely locates at "https://github.com/hfang-bristol/RDataCentre/blob/master/dcGOR" and "http://dcgor.r-forge.r-project.org/data". For the user equipped with fast internet connection, this option can be just left as default. But it is always advisable to download these files locally. Especially when the user needs to run this function many times, there is no need to ask the function to remotely download every time (also it will unnecessarily increase the runtime). For examples, these files (as a whole or part of them) can be first downloaded into your current working directory, and then set this option as: RData.location=".". If RData to load is already part of package itself, this parameter can be ignored (since this function will try to load it via function data first). Here is the UNIX command for downloading all RData files (preserving the directory structure): wget -r -l2 -A "*.RData" -np -nH --cut-dirs=0 "http://dcgor.r-forge.r-project.org/data"

Value

an object of S4 class Eoutput, with following slots:

  • domain: a character specifying the domain identity
  • ontology: a character specifying the ontology used
  • term_info: a matrix of nTerm X 5 containing term information, where nTerm is the number of terms in consideration, and the 5 columns are "term_id" (i.e. "Term ID"), "term_name" (i.e. "Term Name"), "namespace" (i.e. "Term Namespace"), "distance" (i.e. "Term Distance") and "IC" (i.e. "Information Content for the term based on annotation frequency by it")
  • anno: a list of terms, each storing annotated domain members (also within the background domains). Always, terms are identified by "term_id" and domain members identified by their ids (e.g. sunids for SCOP domains)
  • data: a vector containing input data in consideration. It is not always the same as the input data as only those mappable and annotatable are retained
  • background: a vector containing background in consideration. It is not always the same as the input background as only those mappable/annotatable are retained
  • overlap: a list of terms, each storing domains overlapped between domains annotated by a term and domains in the input data (i.e. the domains of interest). Always, terms are identified by "term_id" and domain members identified by their IDs (e.g. sunids for SCOP domains)
  • zscore: a vector containing z-scores
  • pvalue: a vector containing p-values
  • adjp: a vector containing adjusted p-values. It is the p value but after being adjusted for multiple comparisons

Note

The interpretation of the algorithms used to account for the hierarchy of the ontology is:

  • "none": does not consider the ontology hierarchy at all.
  • "lea": computers the significance of a term in terms of the significance of its children at the maximum depth (e.g. 2). Precisely, once domains are already annotated to any children terms with a more signficance than itself, then all these domains are eliminated from the use for the recalculation of the signifance at that term. The final p-values takes the maximum of the original p-value and the recalculated p-value.
  • "elim": computers the significance of a term in terms of the significance of its all children. Precisely, once domains are already annotated to a signficantly enriched term under the cutoff of e.g. pvalue<1e-2, all these domains are eliminated from the ancestors of that term).
  • "pc": requires the significance of a term not only using the whole domains as background but also using domains annotated to all its direct parents/ancestors as background. The final p-value takes the maximum of both p-values in these two calculations.
  • "Notes": the order of the number of significant terms is: "none" > "lea" > "elim" > "pc".

Examples

# 1) Enrichment analysis for SCOP domain superfamilies (sf)
## 1a) load SCOP.sf (as 'InfoDataFrame' object)
SCOP.sf <- dcRDataLoader('SCOP.sf')


'SCOP.sf' (from package 'dcGOR' version 1.0.5) has been loaded into the working environment

### randomly select 50 domains as a list of domains of interest
data <- sample(rowNames(SCOP.sf), 50)
## 1b) perform enrichment analysis, producing an object of S4 class 'Eoutput'
eoutput <- dcEnrichment(data, domain="SCOP.sf", ontology="GOMF")


Start at 2015-07-23 12:50:56

First, load the ontology 'GOMF', the domain 'SCOP.sf', and their associations (2015-07-23 12:50:56) ...
'onto.GOMF' (from package 'dcGOR' version 1.0.5) has been loaded into the working environment
'SCOP.sf' (from package 'dcGOR' version 1.0.5) has been loaded into the working environment
'SCOP.sf2GOMF' (from package 'dcGOR' version 1.0.5) has been loaded into the working environment
Second, perform enrichment analysis using HypergeoTest (2015-07-23 12:51:24) ...
	There are 811 terms being used, each restricted within [10,1000] annotations
Last, adjust the p-values using the BH method (2015-07-23 12:51:24) ...

End at 2015-07-23 12:51:24
Runtime in total is: 28 secs


eoutput



An object of S4 class 'Eoutput', containing following slots:
  @domain: 'SCOP.sf'
  @ontology: 'GOMF'
  @term_info: a data.frame of 162 terms X 5 information
  @anno: a list of 162 terms, each storing annotated domains
  @data: a vector containing a group of 25 input domains (annotatable)
  @background: a vector containing a group of 1083 background domains (annotatable)
  @overlap: a list of 162 terms, each containing domains overlapped with input domains
  @zscore: a vector of 162 terms, containing z-scores
  @pvalue: a vector of 162 terms, containing p-values
  @adjp: a vector of 162 terms, containing adjusted p-values
In summary, a total of 162 terms ('GOMF') are analysed for a group of 25 input domains ('SCOP.sf')



## 1c) view the top 10 significance terms
view(eoutput, top_num=10, sortBy="pvalue", details=TRUE)



              term_id nAnno nGroup nOverlap zscore pvalue adjp
GO:0008066 GO:0008066    40     25        3   2.23  0.012 0.49
GO:0008238 GO:0008238    65     25        4   2.13  0.014 0.49
GO:1901363 GO:1901363   487     25       16   1.93  0.016 0.49
GO:0097159 GO:0097159   492     25       16   1.89  0.018 0.49
GO:0035014 GO:0035014    98     25        5   1.93  0.020 0.49
GO:0005275 GO:0005275    57     25        3   1.53  0.038 0.49
GO:0005488 GO:0005488   887     25       23   1.33  0.043 0.49
GO:0030234 GO:0030234   408     25       13   1.49  0.046 0.49
GO:0022804 GO:0022804   369     25       12   1.49  0.047 0.49
GO:0005319 GO:0005319   184     25        7   1.48  0.047 0.49
                                                  term_name     term_namespace
GO:0008066                      glutamate receptor activity molecular_function
GO:0008238                            exopeptidase activity molecular_function
GO:1901363                    heterocyclic compound binding molecular_function
GO:0097159                  organic cyclic compound binding molecular_function
GO:0035014 phosphatidylinositol 3-kinase regulator activity molecular_function
GO:0005275         amine transmembrane transporter activity molecular_function
GO:0005488                                          binding molecular_function
GO:0030234                        enzyme regulator activity molecular_function
GO:0022804        active transmembrane transporter activity molecular_function
GO:0005319                       lipid transporter activity molecular_function
           term_distance
GO:0008066             5
GO:0008238             5
GO:1901363             2
GO:0097159             2
GO:0035014             3
GO:0005275             4
GO:0005488             1
GO:0030234             1
GO:0022804             3
GO:0005319             3
                                                                                                                                                  members
GO:0008066                                                                                                                              52743,49854,54768
GO:0008238                                                                                                                       51182,48264,54768,144217
GO:1901363                                              52029,52440,56024,109880,63763,52949,48264,55144,103637,49329,55287,47027,52743,52777,49854,54768
GO:0097159                                              52029,52440,56024,109880,63763,52949,48264,55144,103637,49329,55287,47027,52743,52777,49854,54768
GO:0035014                                                                                                                63763,51182,49329,109640,144217
GO:0005275                                                                                                                              56024,55144,52777
GO:0005488 48113,52029,52440,56024,109880,63763,52949,47668,51182,75620,48264,55144,103637,49329,109640,101353,55287,47027,52743,52777,49854,54768,144217
GO:0030234                                                               48113,52029,52440,56024,63763,51182,48264,103637,49329,109640,52743,49854,144217
GO:0022804                                                                      46906,52029,52440,56024,109880,63763,75620,55144,103637,52743,52777,54768
GO:0005319                                                                                                      48113,52029,52440,48264,49329,52777,54768



## 1d) visualise the top 10 significant terms in the ontology hierarchy
### color-coded according to 10-based negative logarithm of adjusted p-values (adjp)
visEnrichment(eoutput)


Ontology 'GOMF' containing 16 nodes/terms (including 5 in query; also highlighted in frame) has been shown in your screen, with colorbar indicating -1*log10(adjusted p-values)


## 1e) the same as above but using a customised background
### randomly select 500 domains as background
background <- sample(rowNames(SCOP.sf), 500)
### perform enrichment analysis, producing an object of S4 class 'Eoutput'
eoutput <- dcEnrichment(data, background=background, domain="SCOP.sf",
ontology="GOMF")


Start at 2015-07-23 12:51:35

First, load the ontology 'GOMF', the domain 'SCOP.sf', and their associations (2015-07-23 12:51:35) ...
'onto.GOMF' (from package 'dcGOR' version 1.0.5) has been loaded into the working environment
'SCOP.sf' (from package 'dcGOR' version 1.0.5) has been loaded into the working environment
'SCOP.sf2GOMF' (from package 'dcGOR' version 1.0.5) has been loaded into the working environment
Second, perform enrichment analysis using HypergeoTest (2015-07-23 12:51:50) ...
	There are 393 terms being used, each restricted within [10,1000] annotations
Last, adjust the p-values using the BH method (2015-07-23 12:51:50) ...

End at 2015-07-23 12:51:50
Runtime in total is: 15 secs


eoutput



An object of S4 class 'Eoutput', containing following slots:
  @domain: 'SCOP.sf'
  @ontology: 'GOMF'
  @term_info: a data.frame of 162 terms X 5 information
  @anno: a list of 162 terms, each storing annotated domains
  @data: a vector containing a group of 25 input domains (annotatable)
  @background: a vector containing a group of 257 background domains (annotatable)
  @overlap: a list of 162 terms, each containing domains overlapped with input domains
  @zscore: a vector of 162 terms, containing z-scores
  @pvalue: a vector of 162 terms, containing p-values
  @adjp: a vector of 162 terms, containing adjusted p-values
In summary, a total of 162 terms ('GOMF') are analysed for a group of 25 input domains ('SCOP.sf')



### view the top 10 significance terms
view(eoutput, top_num=10, sortBy="pvalue", details=TRUE)



              term_id nAnno nGroup nOverlap zscore pvalue adjp
GO:0008066 GO:0008066    11     25        3   2.00  0.015 0.56
GO:0008238 GO:0008238    17     25        4   1.98  0.016 0.56
GO:1901363 GO:1901363   118     25       16   1.91  0.017 0.56
GO:0005275 GO:0005275    12     25        3   1.82  0.020 0.56
GO:0097159 GO:0097159   121     25       16   1.78  0.023 0.56
GO:0015662 GO:0015662    13     25        3   1.66  0.027 0.56
GO:0016796 GO:0016796    15     25        3   1.38  0.046 0.56
GO:0022804 GO:0022804    89     25       12   1.48  0.047 0.56
GO:0030234 GO:0030234    99     25       13   1.45  0.049 0.56
GO:0005515 GO:0005515   164     25       19   1.33  0.056 0.56
                                                                                                      term_name
GO:0008066                                                                          glutamate receptor activity
GO:0008238                                                                                exopeptidase activity
GO:1901363                                                                        heterocyclic compound binding
GO:0005275                                                             amine transmembrane transporter activity
GO:0097159                                                                      organic cyclic compound binding
GO:0015662                ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism
GO:0016796 exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomon
GO:0022804                                                            active transmembrane transporter activity
GO:0030234                                                                            enzyme regulator activity
GO:0005515                                                                                      protein binding
               term_namespace term_distance
GO:0008066 molecular_function             5
GO:0008238 molecular_function             5
GO:1901363 molecular_function             2
GO:0005275 molecular_function             4
GO:0097159 molecular_function             2
GO:0015662 molecular_function            12
GO:0016796 molecular_function             6
GO:0022804 molecular_function             3
GO:0030234 molecular_function             1
GO:0005515 molecular_function             2
                                                                                                                        members
GO:0008066                                                                                                    54768,52743,49854
GO:0008238                                                                                             54768,51182,48264,144217
GO:1901363                    55287,103637,54768,48264,49329,63763,52440,52743,47027,52949,56024,55144,52777,49854,109880,52029
GO:0005275                                                                                                    56024,55144,52777
GO:0097159                    55287,103637,54768,48264,49329,63763,52440,52743,47027,52949,56024,55144,52777,49854,109880,52029
GO:0015662                                                                                                   103637,54768,63763
GO:0016796                                                                                                    54768,75620,52777
GO:0022804                                            103637,54768,63763,52440,52743,75620,56024,55144,52777,109880,52029,46906
GO:0030234                                     103637,51182,48264,49329,63763,52440,144217,109640,52743,56024,48113,49854,52029
GO:0005515 55287,103637,54768,51182,48264,49329,63763,52440,144217,109640,52743,47027,75620,56024,55144,52777,48113,49854,52029



### visualise the top 10 significant terms in the ontology hierarchy
### color-coded according to 10-based negative logarithm of adjusted p-values (adjp)
visEnrichment(eoutput)


Ontology 'GOMF' containing 19 nodes/terms (including 5 in query; also highlighted in frame) has been shown in your screen, with colorbar indicating -1*log10(adjusted p-values)



###########################################################
# 2) Enrichment analysis for Pfam domains (Pfam)
## 2a) load Pfam (as 'InfoDataFrame' object)
Pfam <- dcRDataLoader('Pfam')


'Pfam' (from package 'dcGOR' version 1.0.5) has been loaded into the working environment

### randomly select 100 domains as a list of domains of interest
data <- sample(rowNames(Pfam), 100)
## 2b) perform enrichment analysis, producing an object of S4 class 'Eoutput'
eoutput <- dcEnrichment(data, domain="Pfam", ontology="GOMF")


Start at 2015-07-23 12:52:05

First, load the ontology 'GOMF', the domain 'Pfam', and their associations (2015-07-23 12:52:05) ...
'onto.GOMF' (from package 'dcGOR' version 1.0.5) has been loaded into the working environment
'Pfam' (from package 'dcGOR' version 1.0.5) has been loaded into the working environment
'Pfam2GOMF' (from package 'dcGOR' version 1.0.5) has been loaded into the working environment
Second, perform enrichment analysis using HypergeoTest (2015-07-23 12:52:20) ...
	There are 334 terms being used, each restricted within [10,1000] annotations
Last, adjust the p-values using the BH method (2015-07-23 12:52:20) ...

End at 2015-07-23 12:52:20
Runtime in total is: 15 secs


eoutput



An object of S4 class 'Eoutput', containing following slots:
  @domain: 'Pfam'
  @ontology: 'GOMF'
  @term_info: a data.frame of 10 terms X 5 information
  @anno: a list of 10 terms, each storing annotated domains
  @data: a vector containing a group of 24 input domains (annotatable)
  @background: a vector containing a group of 3359 background domains (annotatable)
  @overlap: a list of 10 terms, each containing domains overlapped with input domains
  @zscore: a vector of 10 terms, containing z-scores
  @pvalue: a vector of 10 terms, containing p-values
  @adjp: a vector of 10 terms, containing adjusted p-values
In summary, a total of 10 terms ('GOMF') are analysed for a group of 24 input domains ('Pfam')



## 2c) view the top 10 significance terms
view(eoutput, top_num=10, sortBy="pvalue", details=TRUE)



              term_id nAnno nGroup nOverlap zscore pvalue adjp
GO:0022891 GO:0022891   273     24        3  0.787   0.13 0.30
GO:0022857 GO:0022857   290     24        3  0.677   0.15 0.30
GO:0016740 GO:0016740   767     24        7  0.742   0.16 0.30
GO:0022892 GO:0022892   296     24        3  0.640   0.16 0.30
GO:0005215 GO:0005215   321     24        3  0.492   0.19 0.30
GO:0016787 GO:0016787   690     24        6  0.542   0.21 0.30
GO:0016772 GO:0016772   332     24        3  0.431   0.21 0.30
GO:0003824 GO:0003824  2241     24       17  0.429   0.26 0.33
GO:0005515 GO:0005515   445     24        3 -0.108   0.40 0.44
GO:0005488 GO:0005488   730     24        4 -0.604   0.62 0.62
                                                                 term_name
GO:0022891           substrate-specific transmembrane transporter activity
GO:0022857                              transmembrane transporter activity
GO:0016740                                            transferase activity
GO:0022892                         substrate-specific transporter activity
GO:0005215                                            transporter activity
GO:0016787                                              hydrolase activity
GO:0016772 transferase activity, transferring phosphorus-containing groups
GO:0003824                                              catalytic activity
GO:0005515                                                 protein binding
GO:0005488                                                         binding
               term_namespace term_distance
GO:0022891 molecular_function             3
GO:0022857 molecular_function             2
GO:0016740 molecular_function             2
GO:0022892 molecular_function             2
GO:0005215 molecular_function             1
GO:0016787 molecular_function             2
GO:0016772 molecular_function             3
GO:0003824 molecular_function             1
GO:0005515 molecular_function             2
GO:0005488 molecular_function             1
                                                                                                                                           members
GO:0022891                                                                                                                 PF00605,PF03573,PF04613
GO:0022857                                                                                                                 PF00605,PF03573,PF04613
GO:0016740                                                                                 PF06214,PF00553,PF06573,PF02117,PF01735,PF01777,PF03007
GO:0022892                                                                                                                 PF00605,PF03573,PF04613
GO:0005215                                                                                                                 PF00605,PF03573,PF04613
GO:0016787                                                                                         PF02812,PF03577,PF00772,PF10255,PF04561,PF04801
GO:0016772                                                                                                                 PF06573,PF02117,PF01735
GO:0003824 PF06214,PF09293,PF02812,PF00553,PF00639,PF03577,PF06573,PF00772,PF02117,PF10255,PF04561,PF03971,PF01735,PF00034,PF01777,PF03007,PF04801
GO:0005515                                                                                                                 PF06293,PF00772,PF00034
GO:0005488                                                                                                         PF06293,PF00772,PF03820,PF00034



## 2d) visualise the top 10 significant terms in the ontology hierarchy
### color-coded according to 10-based negative logarithm of adjusted p-values (adjp)
visEnrichment(eoutput)


Ontology 'GOMF' containing 7 nodes/terms (including 5 in query; also highlighted in frame) has been shown in your screen, with colorbar indicating -1*log10(adjusted p-values)


## 2e) the same as above but using a customised background
### randomly select 1000 domains as background
background <- sample(rowNames(Pfam), 1000)
### perform enrichment analysis, producing an object of S4 class 'Eoutput'
eoutput <- dcEnrichment(data, background=background, domain="Pfam",
ontology="GOMF")


Start at 2015-07-23 12:52:30

First, load the ontology 'GOMF', the domain 'Pfam', and their associations (2015-07-23 12:52:30) ...
'onto.GOMF' (from package 'dcGOR' version 1.0.5) has been loaded into the working environment
'Pfam' (from package 'dcGOR' version 1.0.5) has been loaded into the working environment
'Pfam2GOMF' (from package 'dcGOR' version 1.0.5) has been loaded into the working environment
Second, perform enrichment analysis using HypergeoTest (2015-07-23 12:52:37) ...
	There are 32 terms being used, each restricted within [10,1000] annotations
Last, adjust the p-values using the BH method (2015-07-23 12:52:37) ...

End at 2015-07-23 12:52:37
Runtime in total is: 7 secs


eoutput



An object of S4 class 'Eoutput', containing following slots:
  @domain: 'Pfam'
  @ontology: 'GOMF'
  @term_info: a data.frame of 10 terms X 5 information
  @anno: a list of 10 terms, each storing annotated domains
  @data: a vector containing a group of 24 input domains (annotatable)
  @background: a vector containing a group of 242 background domains (annotatable)
  @overlap: a list of 10 terms, each containing domains overlapped with input domains
  @zscore: a vector of 10 terms, containing z-scores
  @pvalue: a vector of 10 terms, containing p-values
  @adjp: a vector of 10 terms, containing adjusted p-values
In summary, a total of 10 terms ('GOMF') are analysed for a group of 24 input domains ('Pfam')



### view the top 10 significance terms
view(eoutput, top_num=10, sortBy="pvalue", details=TRUE)



              term_id nAnno nGroup nOverlap  zscore pvalue adjp
GO:0016787 GO:0016787    42     24        6  1.0400  0.097 0.32
GO:0016772 GO:0016772    22     24        3  0.6110  0.160 0.32
GO:0022857 GO:0022857    23     24        3  0.5260  0.180 0.32
GO:0022892 GO:0022892    23     24        3  0.5260  0.180 0.32
GO:0022891 GO:0022891    23     24        3  0.5260  0.180 0.32
GO:0005215 GO:0005215    25     24        3  0.3670  0.220 0.32
GO:0016740 GO:0016740    60     24        7  0.5220  0.220 0.32
GO:0003824 GO:0003824   166     24       17  0.2480  0.320 0.40
GO:0005515 GO:0005515    31     24        3 -0.0478  0.370 0.41
GO:0005488 GO:0005488    50     24        4 -0.5080  0.580 0.58
                                                                 term_name
GO:0016787                                              hydrolase activity
GO:0016772 transferase activity, transferring phosphorus-containing groups
GO:0022857                              transmembrane transporter activity
GO:0022892                         substrate-specific transporter activity
GO:0022891           substrate-specific transmembrane transporter activity
GO:0005215                                            transporter activity
GO:0016740                                            transferase activity
GO:0003824                                              catalytic activity
GO:0005515                                                 protein binding
GO:0005488                                                         binding
               term_namespace term_distance
GO:0016787 molecular_function             2
GO:0016772 molecular_function             3
GO:0022857 molecular_function             2
GO:0022892 molecular_function             2
GO:0022891 molecular_function             3
GO:0005215 molecular_function             1
GO:0016740 molecular_function             2
GO:0003824 molecular_function             1
GO:0005515 molecular_function             2
GO:0005488 molecular_function             1
                                                                                                                                           members
GO:0016787                                                                                         PF10255,PF04801,PF00772,PF03577,PF02812,PF04561
GO:0016772                                                                                                                 PF06573,PF02117,PF01735
GO:0022857                                                                                                                 PF04613,PF00605,PF03573
GO:0022892                                                                                                                 PF04613,PF00605,PF03573
GO:0022891                                                                                                                 PF04613,PF00605,PF03573
GO:0005215                                                                                                                 PF04613,PF00605,PF03573
GO:0016740                                                                                 PF06573,PF06214,PF03007,PF00553,PF02117,PF01777,PF01735
GO:0003824 PF10255,PF00639,PF04801,PF06573,PF06214,PF00772,PF00034,PF03007,PF03577,PF00553,PF03971,PF02812,PF09293,PF02117,PF04561,PF01777,PF01735
GO:0005515                                                                                                                 PF00772,PF00034,PF06293
GO:0005488                                                                                                         PF03820,PF00772,PF00034,PF06293



### visualise the top 10 significant terms in the ontology hierarchy
### color-coded according to 10-based negative logarithm of adjusted p-values (adjp)
visEnrichment(eoutput)


Ontology 'GOMF' containing 9 nodes/terms (including 5 in query; also highlighted in frame) has been shown in your screen, with colorbar indicating -1*log10(adjusted p-values)



###########################################################
# 3) Enrichment analysis for InterPro domains (InterPro)
## 3a) load InterPro (as 'InfoDataFrame' object)
InterPro <- dcRDataLoader('InterPro')


'InterPro' (from package 'dcGOR' version 1.0.5) has been loaded into the working environment

### randomly select 100 domains as a list of domains of interest
data <- sample(rowNames(InterPro), 100)
## 3b) perform enrichment analysis, producing an object of S4 class 'Eoutput'
eoutput <- dcEnrichment(data, domain="InterPro", ontology="GOMF")


Start at 2015-07-23 12:52:51

First, load the ontology 'GOMF', the domain 'InterPro', and their associations (2015-07-23 12:52:51) ...
'onto.GOMF' (from package 'dcGOR' version 1.0.5) has been loaded into the working environment
'InterPro' (from package 'dcGOR' version 1.0.5) has been loaded into the working environment
'InterPro2GOMF' (from package 'dcGOR' version 1.0.5) has been loaded into the working environment
Second, perform enrichment analysis using HypergeoTest (2015-07-23 12:53:15) ...
	There are 630 terms being used, each restricted within [10,1000] annotations
Last, adjust the p-values using the BH method (2015-07-23 12:53:15) ...

End at 2015-07-23 12:53:15
Runtime in total is: 24 secs


eoutput



An object of S4 class 'Eoutput', containing following slots:
  @domain: 'InterPro'
  @ontology: 'GOMF'
  @term_info: a data.frame of 65 terms X 5 information
  @anno: a list of 65 terms, each storing annotated domains
  @data: a vector containing a group of 79 input domains (annotatable)
  @background: a vector containing a group of 8899 background domains (annotatable)
  @overlap: a list of 65 terms, each containing domains overlapped with input domains
  @zscore: a vector of 65 terms, containing z-scores
  @pvalue: a vector of 65 terms, containing p-values
  @adjp: a vector of 65 terms, containing adjusted p-values
In summary, a total of 65 terms ('GOMF') are analysed for a group of 79 input domains ('InterPro')



## 3c) view the top 10 significance terms
view(eoutput, top_num=10, sortBy="pvalue", details=TRUE)



              term_id nAnno nGroup nOverlap zscore pvalue adjp
GO:0016814 GO:0016814    37     79        3   4.69 0.0003 0.02
GO:0015631 GO:0015631    72     79        3   2.98 0.0037 0.10
GO:0016879 GO:0016879   136     79        4   2.57 0.0071 0.10
GO:0008092 GO:0008092    88     79        3   2.53 0.0076 0.10
GO:0004857 GO:0004857    89     79        3   2.51 0.0079 0.10
GO:1901981 GO:1901981   210     79        5   2.33 0.0110 0.12
GO:0016874 GO:0016874   234     79        5   2.06 0.0170 0.14
GO:0035091 GO:0035091   236     79        5   2.04 0.0180 0.14
GO:0005543 GO:0005543   239     79        5   2.01 0.0190 0.14
GO:0016810 GO:0016810   250     79        5   1.90 0.0230 0.15
                                                                                           term_name
GO:0016814 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines
GO:0015631                                                                           tubulin binding
GO:0016879                                            ligase activity, forming carbon-nitrogen bonds
GO:0008092                                                              cytoskeletal protein binding
GO:0004857                                                                 enzyme inhibitor activity
GO:1901981                                                    phosphatidylinositol phosphate binding
GO:0016874                                                                           ligase activity
GO:0035091                                                              phosphatidylinositol binding
GO:0005543                                                                      phospholipid binding
GO:0016810                     hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds
               term_namespace term_distance
GO:0016814 molecular_function             4
GO:0015631 molecular_function             4
GO:0016879 molecular_function             3
GO:0008092 molecular_function             3
GO:0004857 molecular_function             2
GO:1901981 molecular_function             6
GO:0016874 molecular_function             2
GO:0035091 molecular_function             5
GO:0005543 molecular_function             3
GO:0016810 molecular_function             3
                                                     members
GO:0016814                     IPR010048,IPR027147,IPR001021
GO:0015631                     IPR001327,IPR001308,IPR026770
GO:0016879           IPR011009,IPR022414,IPR015911,IPR008055
GO:0008092                     IPR001327,IPR001308,IPR026770
GO:0004857                     IPR007312,IPR006932,IPR003175
GO:1901981 IPR028382,IPR011804,IPR004044,IPR001890,IPR003286
GO:0016874 IPR011009,IPR022414,IPR015911,IPR017427,IPR008055
GO:0035091 IPR028382,IPR011804,IPR004044,IPR001890,IPR003286
GO:0005543 IPR028382,IPR011804,IPR004044,IPR001890,IPR003286
GO:0016810 IPR010801,IPR010048,IPR010052,IPR027147,IPR001021



## 3d) visualise the top 10 significant terms in the ontology hierarchy
### color-coded according to 10-based negative logarithm of adjusted p-values (adjp)
visEnrichment(eoutput)


Ontology 'GOMF' containing 13 nodes/terms (including 5 in query; also highlighted in frame) has been shown in your screen, with colorbar indicating -1*log10(adjusted p-values)


## 3e) the same as above but using a customised background
### randomly select 1000 domains as background
background <- sample(rowNames(InterPro), 1000)
### perform enrichment analysis, producing an object of S4 class 'Eoutput'
eoutput <- dcEnrichment(data, background=background, domain="InterPro",
ontology="GOMF")


Start at 2015-07-23 12:53:25

First, load the ontology 'GOMF', the domain 'InterPro', and their associations (2015-07-23 12:53:25) ...
'onto.GOMF' (from package 'dcGOR' version 1.0.5) has been loaded into the working environment
'InterPro' (from package 'dcGOR' version 1.0.5) has been loaded into the working environment
'InterPro2GOMF' (from package 'dcGOR' version 1.0.5) has been loaded into the working environment
Second, perform enrichment analysis using HypergeoTest (2015-07-23 12:53:41) ...
	There are 136 terms being used, each restricted within [10,1000] annotations
Last, adjust the p-values using the BH method (2015-07-23 12:53:41) ...

End at 2015-07-23 12:53:41
Runtime in total is: 16 secs


eoutput



An object of S4 class 'Eoutput', containing following slots:
  @domain: 'InterPro'
  @ontology: 'GOMF'
  @term_info: a data.frame of 64 terms X 5 information
  @anno: a list of 64 terms, each storing annotated domains
  @data: a vector containing a group of 79 input domains (annotatable)
  @background: a vector containing a group of 831 background domains (annotatable)
  @overlap: a list of 64 terms, each containing domains overlapped with input domains
  @zscore: a vector of 64 terms, containing z-scores
  @pvalue: a vector of 64 terms, containing p-values
  @adjp: a vector of 64 terms, containing adjusted p-values
In summary, a total of 64 terms ('GOMF') are analysed for a group of 79 input domains ('InterPro')



### view the top 10 significance terms
view(eoutput, top_num=10, sortBy="pvalue", details=TRUE)



              term_id nAnno nGroup nOverlap zscore pvalue adjp
GO:1901981 GO:1901981    19     79        5   2.53 0.0061 0.13
GO:0035091 GO:0035091    20     79        5   2.39 0.0080 0.13
GO:0016810 GO:0016810    21     79        5   2.26 0.0100 0.13
GO:0005543 GO:0005543    22     79        5   2.14 0.0130 0.13
GO:0005488 GO:0005488   153     79       21   1.97 0.0200 0.13
GO:0043167 GO:0043167    60     79       10   1.96 0.0200 0.13
GO:0004857 GO:0004857    12     79        3   1.84 0.0210 0.13
GO:0015631 GO:0015631    12     79        3   1.84 0.0210 0.13
GO:0043168 GO:0043168    53     79        9   1.92 0.0220 0.13
GO:0016879 GO:0016879    18     79        4   1.86 0.0220 0.13
                                                                       term_name
GO:1901981                                phosphatidylinositol phosphate binding
GO:0035091                                          phosphatidylinositol binding
GO:0016810 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds
GO:0005543                                                  phospholipid binding
GO:0005488                                                               binding
GO:0043167                                                           ion binding
GO:0004857                                             enzyme inhibitor activity
GO:0015631                                                       tubulin binding
GO:0043168                                                         anion binding
GO:0016879                        ligase activity, forming carbon-nitrogen bonds
               term_namespace term_distance
GO:1901981 molecular_function             6
GO:0035091 molecular_function             5
GO:0016810 molecular_function             3
GO:0005543 molecular_function             3
GO:0005488 molecular_function             1
GO:0043167 molecular_function             2
GO:0004857 molecular_function             2
GO:0015631 molecular_function             4
GO:0043168 molecular_function             3
GO:0016879 molecular_function             3
                                                                                                                                                                                                                     members
GO:1901981                                                                                                                                                                 IPR004044,IPR028382,IPR011804,IPR003286,IPR001890
GO:0035091                                                                                                                                                                 IPR004044,IPR028382,IPR011804,IPR003286,IPR001890
GO:0016810                                                                                                                                                                 IPR010052,IPR001021,IPR027147,IPR010048,IPR010801
GO:0005543                                                                                                                                                                 IPR004044,IPR028382,IPR011804,IPR003286,IPR001890
GO:0005488 IPR001308,IPR012758,IPR004044,IPR028382,IPR026770,IPR020469,IPR006335,IPR005101,IPR029325,IPR000681,IPR015570,IPR011804,IPR000957,IPR008757,IPR002653,IPR023957,IPR017375,IPR017427,IPR003286,IPR001327,IPR001890
GO:0043167                                                                                                               IPR012758,IPR004044,IPR028382,IPR015570,IPR011804,IPR002653,IPR017375,IPR017427,IPR003286,IPR001890
GO:0004857                                                                                                                                                                                     IPR003175,IPR007312,IPR006932
GO:0015631                                                                                                                                                                                     IPR001308,IPR026770,IPR001327
GO:0043168                                                                                                                         IPR012758,IPR004044,IPR028382,IPR015570,IPR011804,IPR002653,IPR017375,IPR003286,IPR001890
GO:0016879                                                                                                                                                                           IPR022414,IPR011009,IPR015911,IPR008055



### visualise the top 10 significant terms in the ontology hierarchy
### color-coded according to 10-based negative logarithm of adjusted p-values (adjp)
visEnrichment(eoutput)


Ontology 'GOMF' containing 9 nodes/terms (including 5 in query; also highlighted in frame) has been shown in your screen, with colorbar indicating -1*log10(adjusted p-values)



###########################################################
# 4) Enrichment analysis for Rfam RNA families (Rfam)
## 4a) load Rfam (as 'InfoDataFrame' object)
Rfam <- dcRDataLoader('Rfam')


'Rfam' (from package 'dcGOR' version 1.0.5) has been loaded into the working environment

### randomly select 100 RNAs as a list of RNAs of interest
data <- sample(rowNames(Rfam), 100)
## 4b) perform enrichment analysis, producing an object of S4 class 'Eoutput'
eoutput <- dcEnrichment(data, domain="Rfam", ontology="GOBP")


Start at 2015-07-23 12:53:58

First, load the ontology 'GOBP', the domain 'Rfam', and their associations (2015-07-23 12:53:58) ...
'onto.GOBP' (from package 'dcGOR' version 1.0.5) has been loaded into the working environment
'Rfam' (from package 'dcGOR' version 1.0.5) has been loaded into the working environment
'Rfam2GOBP' (from package 'dcGOR' version 1.0.5) has been loaded into the working environment
Second, perform enrichment analysis using HypergeoTest (2015-07-23 12:54:06) ...
	There are 114 terms being used, each restricted within [10,1000] annotations
Last, adjust the p-values using the BH method (2015-07-23 12:54:06) ...

End at 2015-07-23 12:54:06
Runtime in total is: 8 secs


eoutput



An object of S4 class 'Eoutput', containing following slots:
  @domain: 'Rfam'
  @ontology: 'GOBP'
  @term_info: a data.frame of 24 terms X 5 information
  @anno: a list of 24 terms, each storing annotated domains
  @data: a vector containing a group of 63 input domains (annotatable)
  @background: a vector containing a group of 1377 background domains (annotatable)
  @overlap: a list of 24 terms, each containing domains overlapped with input domains
  @zscore: a vector of 24 terms, containing z-scores
  @pvalue: a vector of 24 terms, containing p-values
  @adjp: a vector of 24 terms, containing adjusted p-values
In summary, a total of 24 terms ('GOBP') are analysed for a group of 63 input domains ('Rfam')



## 4c) view the top 10 significance terms
view(eoutput, top_num=10, sortBy="pvalue", details=FALSE)



              term_id nAnno nGroup nOverlap  zscore pvalue adjp
GO:0050794 GO:0050794    61     63        5  1.3800  0.056 0.86
GO:0050789 GO:0050789    81     63        5  0.7090  0.160 0.86
GO:0065007 GO:0065007    85     63        5  0.5950  0.190 0.86
GO:0000376 GO:0000376   522     63       25  0.2970  0.330 0.86
GO:0000372 GO:0000372   522     63       25  0.2970  0.330 0.86
GO:0008380 GO:0008380   542     63       25  0.0535  0.420 0.86
GO:0000375 GO:0000375   541     63       25  0.0656  0.420 0.86
GO:0006396 GO:0006396  1225     63       55 -0.4300  0.610 0.86
GO:0016070 GO:0016070  1237     63       55 -0.6800  0.690 0.86
GO:0090304 GO:0090304  1239     63       55 -0.7240  0.710 0.86
                                                                               term_name
GO:0050794                                                regulation of cellular process
GO:0050789                                              regulation of biological process
GO:0065007                                                         biological regulation
GO:0000376 RNA splicing, via transesterification reactions with guanosine as nucleophile
GO:0000372                                                       Group I intron splicing
GO:0008380                                                                  RNA splicing
GO:0000375                               RNA splicing, via transesterification reactions
GO:0006396                                                                RNA processing
GO:0016070                                                         RNA metabolic process
GO:0090304                                                nucleic acid metabolic process



## 4d) visualise the top 10 significant terms in the ontology hierarchy
### color-coded according to 10-based negative logarithm of adjusted p-values (adjp)
visEnrichment(eoutput)


Ontology 'GOBP' containing 17 nodes/terms (including 5 in query; also highlighted in frame) has been shown in your screen, with colorbar indicating -1*log10(adjusted p-values)


## 4e) the same as above but using a customised background
### randomly select 1000 RNAs as background
background <- sample(rowNames(Rfam), 1000)
### perform enrichment analysis, producing an object of S4 class 'Eoutput'
eoutput <- dcEnrichment(data, background=background, domain="Rfam",
ontology="GOBP")


Start at 2015-07-23 12:54:47

First, load the ontology 'GOBP', the domain 'Rfam', and their associations (2015-07-23 12:54:47) ...
'onto.GOBP' (from package 'dcGOR' version 1.0.5) has been loaded into the working environment
'Rfam' (from package 'dcGOR' version 1.0.5) has been loaded into the working environment
'Rfam2GOBP' (from package 'dcGOR' version 1.0.5) has been loaded into the working environment
Second, perform enrichment analysis using HypergeoTest (2015-07-23 12:54:56) ...
	There are 62 terms being used, each restricted within [10,1000] annotations
Last, adjust the p-values using the BH method (2015-07-23 12:54:56) ...

End at 2015-07-23 12:54:56
Runtime in total is: 9 secs


eoutput



An object of S4 class 'Eoutput', containing following slots:
  @domain: 'Rfam'
  @ontology: 'GOBP'
  @term_info: a data.frame of 24 terms X 5 information
  @anno: a list of 24 terms, each storing annotated domains
  @data: a vector containing a group of 63 input domains (annotatable)
  @background: a vector containing a group of 650 background domains (annotatable)
  @overlap: a list of 24 terms, each containing domains overlapped with input domains
  @zscore: a vector of 24 terms, containing z-scores
  @pvalue: a vector of 24 terms, containing p-values
  @adjp: a vector of 24 terms, containing adjusted p-values
In summary, a total of 24 terms ('GOBP') are analysed for a group of 63 input domains ('Rfam')



### view the top 10 significance terms
view(eoutput, top_num=10, sortBy="pvalue", details=FALSE)



              term_id nAnno nGroup nOverlap zscore pvalue adjp
GO:0050794 GO:0050794    36     63        5  0.875   0.12 0.89
GO:0050789 GO:0050789    43     63        5  0.444   0.23 0.89
GO:0065007 GO:0065007    45     63        5  0.333   0.26 0.89
GO:0000376 GO:0000376   240     63       25  0.477   0.27 0.89
GO:0000372 GO:0000372   240     63       25  0.477   0.27 0.89
GO:0000375 GO:0000375   249     63       25  0.236   0.35 0.89
GO:0008380 GO:0008380   250     63       25  0.209   0.36 0.89
GO:0006396 GO:0006396   576     63       55 -0.345   0.57 0.89
GO:0016070 GO:0016070   578     63       55 -0.431   0.60 0.89
GO:0090304 GO:0090304   580     63       55 -0.519   0.64 0.89
                                                                               term_name
GO:0050794                                                regulation of cellular process
GO:0050789                                              regulation of biological process
GO:0065007                                                         biological regulation
GO:0000376 RNA splicing, via transesterification reactions with guanosine as nucleophile
GO:0000372                                                       Group I intron splicing
GO:0000375                               RNA splicing, via transesterification reactions
GO:0008380                                                                  RNA splicing
GO:0006396                                                                RNA processing
GO:0016070                                                         RNA metabolic process
GO:0090304                                                nucleic acid metabolic process



### visualise the top 10 significant terms in the ontology hierarchy
### color-coded according to 10-based negative logarithm of adjusted p-values (adjp)
visEnrichment(eoutput)


Ontology 'GOBP' containing 17 nodes/terms (including 5 in query; also highlighted in frame) has been shown in your screen, with colorbar indicating -1*log10(adjusted p-values)


###########################################################
# 5) Advanced usage: customised data for domain, ontology and annotations
# 5a) create domain, ontology and annotations
## for domain
domain <-
dcBuildInfoDataFrame(input.file="http://dcgor.r-forge.r-project.org/data/InterPro/InterPro.txt",
output.file="domain.RData")


An object of S4 class 'InfoDataFrame' has been built and saved into '/Users/hfang/Sites/SUPERFAMILY/dcGO/dcGOR/domain.RData'.

## for ontology
dcBuildOnto(relations.file="http://dcgor.r-forge.r-project.org/data/onto/igraph_GOMF_edges.txt",
nodes.file="http://dcgor.r-forge.r-project.org/data/onto/igraph_GOMF_nodes.txt",
output.file="ontology.RData")


An object of S4 class 'Onto' has been built and saved into '/Users/hfang/Sites/SUPERFAMILY/dcGO/dcGOR/ontology.RData'.

## for annotations
dcBuildAnno(domain_info.file="http://dcgor.r-forge.r-project.org/data/InterPro/InterPro.txt",
term_info.file="http://dcgor.r-forge.r-project.org/data/InterPro/GO.txt",
association.file="http://dcgor.r-forge.r-project.org/data/InterPro/Domain2GOMF.txt",
output.file="annotations.RData")


An object of S4 class 'Anno' has been built and saved into '/Users/hfang/Sites/SUPERFAMILY/dcGO/dcGOR/annotations.RData'.

## 5b) prepare data and background
### randomly select 100 domains as a list of domains of interest
data <- sample(rowNames(domain), 100)
### randomly select 1000 domains as background
background <- sample(rowNames(domain), 1000)
## 5c) perform enrichment analysis, producing an object of S4 class 'Eoutput'
eoutput <- dcEnrichment(data, background=background,
domain.RData='domain.RData', ontology.RData='ontology.RData',
annotations.RData='annotations.RData')


Start at 2015-07-23 12:55:42

First, load customised ontology 'ontology.RData', the domain 'domain.RData', and their associations 'annotations.RData' (2015-07-23 12:55:42)...
Second, perform enrichment analysis using HypergeoTest (2015-07-23 12:56:04) ...
	There are 143 terms being used, each restricted within [10,1000] annotations
Last, adjust the p-values using the BH method (2015-07-23 12:56:04) ...

End at 2015-07-23 12:56:04
Runtime in total is: 22 secs


eoutput



An object of S4 class 'Eoutput', containing following slots:
  @domain: 'domain.RData'
  @ontology: 'ontology.RData'
  @term_info: a data.frame of 61 terms X 5 information
  @anno: a list of 61 terms, each storing annotated domains
  @data: a vector containing a group of 79 input domains (annotatable)
  @background: a vector containing a group of 852 background domains (annotatable)
  @overlap: a list of 61 terms, each containing domains overlapped with input domains
  @zscore: a vector of 61 terms, containing z-scores
  @pvalue: a vector of 61 terms, containing p-values
  @adjp: a vector of 61 terms, containing adjusted p-values
In summary, a total of 61 terms ('ontology.RData') are analysed for a group of 79 input domains ('domain.RData')



## 5d) view the top 10 significance terms
view(eoutput, top_num=10, sortBy="pvalue", details=TRUE)



              term_id nAnno nGroup nOverlap zscore pvalue adjp
GO:0016301 GO:0016301    49     79       10   2.77 0.0034 0.21
GO:0008233 GO:0008233    10     79        3   2.27 0.0093 0.24
GO:0016860 GO:0016860    11     79        3   2.07 0.0140 0.24
GO:0030234 GO:0030234    20     79        4   1.67 0.0310 0.24
GO:0016773 GO:0016773    42     79        7   1.69 0.0330 0.24
GO:0015181 GO:0015181    51     79        8   1.63 0.0380 0.24
GO:0015174 GO:0015174    51     79        8   1.63 0.0380 0.24
GO:0016772 GO:0016772    77     79       11   1.59 0.0430 0.24
GO:0004672 GO:0004672    30     79        5   1.42 0.0510 0.24
GO:0004713 GO:0004713    16     79        3   1.32 0.0530 0.24
                                                                 term_name
GO:0016301                                                 kinase activity
GO:0008233                                              peptidase activity
GO:0016860                          intramolecular oxidoreductase activity
GO:0030234                                       enzyme regulator activity
GO:0016773          phosphotransferase activity, alcohol group as acceptor
GO:0015181                     arginine transmembrane transporter activity
GO:0015174             basic amino acid transmembrane transporter activity
GO:0016772 transferase activity, transferring phosphorus-containing groups
GO:0004672                                         protein kinase activity
GO:0004713                                protein tyrosine kinase activity
               term_namespace term_distance
GO:0016301 molecular_function             4
GO:0008233 molecular_function             3
GO:0016860 molecular_function             3
GO:0030234 molecular_function             1
GO:0016773 molecular_function             4
GO:0015181 molecular_function             6
GO:0015174 molecular_function             9
GO:0016772 molecular_function             3
GO:0004672 molecular_function             5
GO:0004713 molecular_function             6
                                                                                                                 members
GO:0016301           IPR012750,IPR005778,IPR011925,IPR024193,IPR006295,IPR022917,IPR002314,IPR010196,IPR023517,IPR027686
GO:0008233                                                                                 IPR013347,IPR005778,IPR012400
GO:0016860                                                                                 IPR012829,IPR009169,IPR019805
GO:0030234                                                                       IPR020455,IPR012686,IPR023489,IPR004628
GO:0016773                                         IPR012750,IPR005778,IPR006295,IPR022917,IPR002314,IPR010196,IPR023517
GO:0015181                               IPR007984,IPR008593,IPR001510,IPR024193,IPR027289,IPR013499,IPR003851,IPR006779
GO:0015174                               IPR007984,IPR008593,IPR001510,IPR024193,IPR027289,IPR013499,IPR003851,IPR006779
GO:0016772 IPR012750,IPR005778,IPR011925,IPR024193,IPR006295,IPR022917,IPR002314,IPR000385,IPR010196,IPR023517,IPR027686
GO:0004672                                                             IPR012750,IPR022917,IPR002314,IPR010196,IPR023517
GO:0004713                                                                                 IPR012750,IPR022917,IPR010196



### visualise the top 10 significant terms in the ontology hierarchy
### color-coded according to 10-based negative logarithm of adjusted p-values (adjp)
visEnrichment(eoutput)


Ontology 'ontology.RData' containing 11 nodes/terms (including 5 in query; also highlighted in frame) has been shown in your screen, with colorbar indicating -1*log10(adjusted p-values)

Source code

dcEnrichment.r

Source man

dcEnrichment.Rd dcEnrichment.pdf

See also

dcRDataLoader, dcDAGannotate, Eoutput-class, visEnrichment, dcConverter