gafreader_class: S4 class for GAFReader object

Description Constructor Accessors Methods Examples

Description

Parser for annotation presented in GAF file format (.gaf). GAFReader function returns object which contains as a dataframe annotation as it presented in initial file. Via GAFReader accessor method one can retrieve annotations as list GO term id's as keys and Gene ID's as values and version of file (see Accessors section).

Constructor

GAFReader(file = gaf_path, geneid_col = 10), where:

file - full path to annotation file

geneid_col - index of column with Gene ID (2 by default)

Accessors

In the code examples below object is an object of GAFReader class

getVersion(object) - returns version of GAF file

getAnnotation(object) - returns annotation from GAF file in form of GO ids - Gene ids list

Methods

In the code examples below object is an object of GAFReader class

getAnnotation(object) - Convert annotation to list contains GO term id's as keys and Gene ID's as values

Examples

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# read .gaf file (in this example gaf file with annotation for \emph{A.thaliana} is used)
# object returned by \code{\link{GAFReader}} can be used by
# \code{\link{FuncAnnotGroupsTopGO}} function.
gaf_path <- system.file("extdata", "gene_association.tair.lzma",
                         package = "FoldGO", mustWork = TRUE)
gaf <- GAFReader(file = gaf_path, geneid_col = 10)
# get version of file
getVersion(gaf)
# get annoitation in the list format contains GO term id's as keys and Gene ID's as values
getAnnotation(gaf)

DanWiebe/FoldGO documentation built on May 1, 2020, 11:02 p.m.