getGOlist: Transform Delimited GO Terms To List

In sanger-pathogens/deago: DEAGO: RNASeq differential expression analysis and GO term enrichment reporter

Description

getGOlist transforms a semi-colon delimited vector of GO terms and their corresponding gene identifiers from a data.frame into a list.

Usage

getGOlist(ann, col)

Arguments

ann	A data.frame containing gene symbols and/or delimited GO terms.
col	An integer representing the index of the column containing GO terms.

Details

The annotation dataframe ann contains gene symbols and/or GO terms associated with the genes in the DESeqDataSet object. Each row in the dataframe represents a gene. The first column contains the identifiers which correspond to the rownames of the DESeqDataSet object.

There then follows one or two further columns depending on whether the annotations consist of only gene symbols, only GO terms or both gene symbols and GO terms. For more information see annotateDataset.

getGOlist requires an annotation dataframe ann and an integer value col which represents the index of the column containing the GO terms. For example, if the GO terms were in column 2: getGOlist(ann,2).

Where there are multiple GO terms for a gene, the individual terms should be semi-colon (;) delimited e.g. GO:0004415;GO:0004415;GO:0004415;.

getGOlist returns a list where the names are the gene idenifiers and the values are the associated GO terms. This format is required for topGO GO term enrichment analysis.

Value

A list of GO terms where names are the associated gene identifiers.

See Also

Other annotation functions: addAnnotationsToDataSet, annotateDataset, getGeneSymbols, importAnnotation

Examples

library(DESeq2)
dds <- makeExampleDESeqDataSet(n=3)
good_ann <- data.frame( genes=rownames(dds),
                        gene_names=letters[1:3],
                        go=c("GO:0000001", "GO:0000001;GO:0000002", ""))
good_ann[] <- lapply(good_ann, as.character)
getGOlist(good_ann, 3)

sanger-pathogens/deago documentation built on May 28, 2019, 8:42 a.m.