importAnnotation: Import Annotation File

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

Description

importAnnotation reads a tab-delimited annotation file containing gene symbols and/or GO terms into a dataframe.

Usage

importAnnotation(file)

Arguments

file	A character string giving the name of the annotation file.

Details

The annotation file is a text file containing gene information. Rows correspond to genes while columns correspond to gene symbols and GO terms that are associated with the genes. The annotation file should not contain a header row.

The first column must contain the gene identifiers which correspond to the row names of the DESeqDataSet object. There doesn't need to be an entry for every gene identifier in the DESeqDataSet but, at least one identifier should be represented.

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. 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;.

Value

A dataframe with annotations.

See Also

Other annotation functions: addAnnotationsToDataSet, annotateDataset, getGOlist, getGeneSymbols

Other import functions: annotateDataset, importConfig, importTargets, readCountData, validateConfig, validateTargets

Examples

## Not run: 
importAnnotaton(annotation_file)

## End(Not run)

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