subsetSwitchAnalyzeRlist: A function which subset all entries in a switchAnalyzeRlist.

Description Usage Arguments Value Author(s) References See Also Examples

View source: R/methods.R

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

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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

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data("exampleSwitchList")

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

kvittingseerup/IsoformSwitchAnalyzeR documentation built on May 12, 2021, 12:25 p.m.