extractGeneExpression: Extract gene counts or abundances from a switchAnalyzeRlist...

In IsoformSwitchAnalyzeR: Identify, Annotate and Visualize Alternative Splicing and Isoform Switches with Functional Consequences from both short- and long-read RNA-seq data.

Description

Extract replicate gene counts or expression from a switchAnalyzeRlist object using all the annotation fixes employed in creating the switchAnalyzeRlist.

Usage

extractGeneExpression(
    switchAnalyzeRlist,
    extractCounts = TRUE
)

Arguments

switchAnalyzeRlist	A switchAnalyzeRlist object.
extractCounts	A logic to indicate whether to extract counts (if TRUE, default) or expression estimates (if FALSE).

Details

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.

Value

A data.frame with the replicate count/abundance estimates.

Author(s)

Kristoffer Vitting-Seerup

References

Vitting-Seerup et al. The Landscape of Isoform Switches in Human Cancers. Mol. Cancer Res. (2017).

Examples

data("exampleSwitchList")

geneCountMatrix <- extractGeneExpression(
    exampleSwitchList,
    extractCounts = TRUE
)

geneExpresionMatrix <- extractGeneExpression(
    exampleSwitchList,
    extractCounts = FALSE
)

IsoformSwitchAnalyzeR documentation built on Nov. 8, 2020, 5:36 p.m.