isoformToGeneExp {IsoformSwitchAnalyzeR} | R Documentation |
This function extract gene expression from isoform expression by for each condition summing the expression of all isoforms belonging to a specific gene.
isoformToGeneExp( isoformRepExpression, isoformGeneAnnotation=NULL, quiet = FALSE )
isoformRepExpression |
A replicate isoform abundace matrix (not log-transformed). The isoform:gene relationship can be provided by either:
Importantly |
isoformGeneAnnotation |
A data.frame or GRange with two (meta) collumns: 'isoform_id' and 'gene_id' indicating the relationship between isoforms and parent gene. |
quiet |
A logic indicating whether to avoid printing progress messages. Default is FALSE |
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")) ### Extract gene info localAnnotaion <- rtracklayer::import(system.file("extdata/example.gtf.gz", package="IsoformSwitchAnalyzeR"))[,c('transcript_id','gene_id')] colnames(localAnnotaion@elementMetadata)[1] <- 'isoform_id' ### Summarize to gene level geneRepCount <- isoformToGeneExp( isoformRepExpression = salmonQuant$counts, isoformGeneAnnotation = localAnnotaion )