Extract replicate gene counts or expression from a switchAnalyzeRlist object using all the annotation fixes employed in creating the switchAnalyzeRlist.
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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.
Vitting-Seerup et al. The Landscape of Isoform Switches in Human Cancers. Mol. Cancer Res. (2017).
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