removeAnnoationData {IsoformSwitchAnalyzeR} | R Documentation |
This function can removes the biological sequence and/or the replicate quantification data from a switchAnalyzeRlist which will significantly reduce the size of the object. This is intended to be used after identification of consequnces of isoform switches (via analyzeSwitchConsequences
) have been done as then these data are not longer needed. It is highly recomended to save a version of the switchAnalyzeRlist with all the annotation before removeing it - typically done with base::saveRDS
or base::save
.
removeAnnoationData( switchAnalyzeRlist, removeBioSeq = TRUE, removeQuantData = TRUE )
switchAnalyzeRlist |
A |
removeBioSeq |
A logical indicating whether to remove biological sequences (nucloetide and amino acid sequences) from the switchAnalyzeRlist. Default is TRUE. |
removeQuantData |
A logic indicating whether to remove replicate quantification data (counts, abundances and isoform fractions) from the switchAnalyzeRlist. Default is TRUE. |
This function returns a data.frame where the first column is the gene id followed by the gene expression in all samples.
Kristoffer Vitting-Seerup
Vitting-Seerup et al. The Landscape of Isoform Switches in Human Cancers. Mol. Cancer Res. (2017).
### Please note # 1) The way of importing files in the following example with # "system.file('pathToFile', package="IsoformSwitchAnalyzeR") is # specialiced to access the sample data in the IsoformSwitchAnalyzeR package # and not somhting you need to do - just supply the string e.g. # "/myAnnotation/isoformsQuantified.gtf" to the functions # 2) importRdata directly supports import of a GTF file - just supply the # path (e.g. "/myAnnotation/isoformsQuantified.gtf") to the isoformExonAnnoation argument ### Import quantifications salmonQuant <- importIsoformExpression(system.file("extdata/", package="IsoformSwitchAnalyzeR")) ### Make design matrix myDesign <- data.frame( sampleID = colnames(salmonQuant$abundance)[-1], condition = gsub('_.*', '', colnames(salmonQuant$abundance)[-1]) ) ### Create switchAnalyzeRlist aSwitchList <- importRdata( isoformCountMatrix = salmonQuant$counts, isoformRepExpression = salmonQuant$abundance, designMatrix = myDesign, isoformExonAnnoation = system.file("extdata/example.gtf.gz", package="IsoformSwitchAnalyzeR") ) names(aSwitchList) ### Remove annotation data aSwitchList <- removeAnnoationData(aSwitchList) names(aSwitchList)