Description

An object of class "InfoDataFrame" that contains information on Pfam domains (Pfam). This data is prepared based on ftp://ftp.sanger.ac.uk/pub/databases/Pfam/current_release/database_files/pfamA.txt.gz.

Usage

data(Pfam)

Value

an object of class InfoDataFrame. It has slots for data and dimLabels:

• data: a data.frame containing information about 14831 domains (in rows), with 3 columns ("id" for Pfam accession ID, and "level" always equals "Pfam", "description" for Pfam description)
• dimLabels: a character describing labels for rows and columns in data

References

Finn et al. (2014) The Pfam protein families database. Nucleic Acids Res, 42(Database issue):D222-D230.

Examples

# load data
data(Pfam)
Pfam

An object of S4 class 'InfoDataFrame'
  rowNames: PF00001 PF00002 PF00003 ... PF15659 PF15660 (14831 total)
  colNames: id level description

# retrieve the dimension
dim(Pfam)

[1] 14831     3

# retrieve names of columns
colNames(Pfam)

[1] "id"          "level"       "description"

# retrieve the first 5 rows of data
Data(Pfam)[1:5,]

             id level
PF00001 PF00001  Pfam
PF00002 PF00002  Pfam
PF00003 PF00003  Pfam
PF00004 PF00004  Pfam
PF00005 PF00005  Pfam
                                                            description
PF00001                     7 transmembrane receptor (rhodopsin family)
PF00002                      7 transmembrane receptor (Secretin family)
PF00003                  7 transmembrane sweet-taste receptor of 3 GCPR
PF00004 ATPase family associated with various cellular activities (AAA)
PF00005                                                 ABC transporter

See also