getAnnotation: Get annotation derived from annotation file

In DanWiebe/FoldGO: Package for Fold-specific GO Terms Recognition

Description

This method allows to retrieve annotation from MgsaSets or GAFReader class object in form of list contains GO term id's as keys and Gene ID's as values

Usage

getAnnotation(object)

## S4 method for signature 'AnnotationReader'
getAnnotation(object)

## S4 method for signature 'list'
getAnnotation(object)

## S4 method for signature 'MgsaSets'
getAnnotation(object)

## S4 method for signature ''NULL''
getAnnotation(object)

Arguments

object

- Object of mgsa package MgsaSets class or FoldGO GAFReader class

Value

list contains GO term id's as keys and Gene ID's as values

Examples

## Not run: 
gaf_path <- system.file("extdata", "gene_association.tair.lzma",
                           package = "FoldGO", mustWork = TRUE)
gaf <- GAFReader(file = gaf_path, geneid_col = 10)
getAnnotation(gaf)

## End(Not run)

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