annotateDataset: Annotate DESeqDataSet

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

Description

annotateDataset reads a tab-delimited annotation file containing gene symbols and/or GO terms into a dataframe which is used to annotate the DESeqDataSet.

Usage

annotateDataset(dds, parameters)

Arguments

dds	A DESeqDataSet object.
parameters	A list containing key/value pairs which define the parameters for the analysis (see importConfig for more information).

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;.

annotateDataset returns a DESeqDataSet with the annotations stored in the object metadata. Gene symbols will be accessible using mcols(dds)$symbol while GO terms will be accessible using metadata(dds)$go where dds represents a DESeqDataSet object.

Value

A DESeqDataSet object with annotations.

See Also

Other annotation functions: addAnnotationsToDataSet, getGOlist, getGeneSymbols, importAnnotation

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

Examples

## Not run: 
annotateDataset(dds, parameters)

## End(Not run)

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