subsetSwitchAnalyzeRlist: A function which subset all entries in 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

This function allows the user to remove data from all entries in a switchAnalyzeRlist about isoforms that are no longer of interest. Note that it retain replicate isoforms information for all isoforms associated with genes containing isoforms in the subset (to enable correction for confounding factors when testing with isoformSwitchTestDEXSeq()).

Usage

subsetSwitchAnalyzeRlist(
    switchAnalyzeRlist,
    subset
)

Arguments

switchAnalyzeRlist	A switchAnalyzeRlist object.
subset	logical expression indicating which rows in the isoformFeatures entry should be keep. The rest of the switchAnalyzeRlist is then reduced to only contain the matching information.

Value

A SwitchAnalyzeRlist only containing information about the isoforms (in their specific comparisons) indicated with TRUE in the .

Author(s)

Kristoffer Vitting-Seerup

References

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

See Also

createSwitchAnalyzeRlist
preFilter

Examples

data("exampleSwitchList")

subsetSwitchAnalyzeRlist(
    switchAnalyzeRlist = exampleSwitchList,
    subset = exampleSwitchList$isoformFeatures$gene_overall_mean > 10
)

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