isoformToGeneExp {IsoformSwitchAnalyzeR} | R Documentation |
This function extract gene count/expression from isoform count/expression by for each condition summing the expression of all isoforms belonging to a specific gene. It can automatically extract the isoform:gene relationship from multiple file-types including GTF/GFF files and isoformSwitchAnalyzeRlists
isoformToGeneExp( isoformRepExpression, isoformGeneAnnotation=NULL, quiet = FALSE )
isoformRepExpression |
A replicate isoform abundance matrix (not log-transformed) with genes as rows and samples as columns. The isoform:gene relationship can be provided by either:
Importantly |
isoformGeneAnnotation |
Can be either of:
|
quiet |
A logic indicating whether to avoid printing progress messages. Default is FALSE |
This function returns a data.frame with gene expression from all samples. The gene_ids will be given in the same way they were presented in the isoformRepExpression
input (as row.names or as a separate column (gene_id))
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")) ### Summarize to gene level via GTF file geneRepCount <- isoformToGeneExp( isoformRepExpression = salmonQuant$counts, isoformGeneAnnotation = system.file("extdata/example.gtf.gz", package="IsoformSwitchAnalyzeR") ) ### Summarize to gene level via data.frame file # get data.frame localAnnotaion <- as.data.frame( mcols( rtracklayer::import( system.file("extdata/example.gtf.gz", package="IsoformSwitchAnalyzeR") ) )[,c('transcript_id','gene_id')] ) colnames(localAnnotaion)[1] <- 'isoform_id' geneRepCount <- isoformToGeneExp( isoformRepExpression = salmonQuant$counts, isoformGeneAnnotation = localAnnotaion ) ### From switchAnalyzeRlist # create design 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"), isoformNtFasta = system.file("extdata/example_isoform_nt.fasta.gz", package="IsoformSwitchAnalyzeR") ) geneRepCount <- isoformToGeneExp( isoformRepExpression = salmonQuant$counts, isoformGeneAnnotation = aSwitchList ) # alternatively use geneRepCount <- extractGeneExpression( aSwitchList, extractCounts = TRUE )