extractGeneExpression {IsoformSwitchAnalyzeR} | R Documentation |
Extract replicate gene counts or expression from a switchAnalyzeRlist object using all the annotation fixes employed in creating the switchAnalyzeRlist.
extractGeneExpression( switchAnalyzeRlist, extractCounts = TRUE )
switchAnalyzeRlist |
A |
extractCounts |
A logic to indicate whether to extract counts (if TRUE, default) or expression estimates (if FALSE). |
The count matrix obtained if extractCounts=TRUE
is the same as would be obtained by running tximport with countsFromAbundance="scaledTPM" which are suitable both for analysis of differential expression and usage.
A data.frame with the replicate count/abundance estimates.
Kristoffer Vitting-Seerup
Vitting-Seerup et al. The Landscape of Isoform Switches in Human Cancers. Mol. Cancer Res. (2017).
data("exampleSwitchList") geneCountMatrix <- extractGeneExpression( exampleSwitchList, extractCounts = TRUE ) geneExpresionMatrix <- extractGeneExpression( exampleSwitchList, extractCounts = FALSE )