R: Removes data not needed after switch identification.

removeAnnoationData {IsoformSwitchAnalyzeR}

R Documentation

Removes data not needed after switch identification.

Description

This function can removes the biological sequence and/or the replicate quantification data from a switchAnalyzeRlist which will significantly reduce the size of the object. This is intended to be used after identification of consequnces of isoform switches (via analyzeSwitchConsequences) have been done as then these data are not longer needed. It is highly recomended to save a version of the switchAnalyzeRlist with all the annotation before removeing it - typically done with base::saveRDS or base::save.

Usage

removeAnnoationData(
    switchAnalyzeRlist,
    removeBioSeq = TRUE,
    removeQuantData = TRUE
)

Arguments

`switchAnalyzeRlist`	A `switchAnalyzeRlist` object where `analyzeSwitchConsequences()` have been run to identify consequences of isoform switches
`removeBioSeq`	A logical indicating whether to remove biological sequences (nucloetide and amino acid sequences) from the switchAnalyzeRlist. Default is TRUE.
`removeQuantData`	A logic indicating whether to remove replicate quantification data (counts, abundances and isoform fractions) from the switchAnalyzeRlist. Default is TRUE.

Value

This function returns a data.frame where the first column is the gene id followed by the gene expression in all samples.

Author(s)

Kristoffer Vitting-Seerup

References

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

Examples

### Please note
# 1) The way of importing files in the following example with
#       "system.file('pathToFile', package="IsoformSwitchAnalyzeR") is
#       specialiced to access the sample data in the IsoformSwitchAnalyzeR package
#       and not somhting you need to do - just supply the string e.g.
#       "/myAnnotation/isoformsQuantified.gtf" to the functions
# 2) importRdata directly supports import of a GTF file - just supply the
#       path (e.g. "/myAnnotation/isoformsQuantified.gtf") to the isoformExonAnnoation argument

### Import quantifications
salmonQuant <- importIsoformExpression(system.file("extdata/", package="IsoformSwitchAnalyzeR"))


### Make design matrix
myDesign <- data.frame(
    sampleID = colnames(salmonQuant$abundance)[-1],
    condition = gsub('_.*', '', colnames(salmonQuant$abundance)[-1])
)

### Create switchAnalyzeRlist
aSwitchList <- importRdata(
    isoformCountMatrix   = salmonQuant$counts,
    isoformRepExpression = salmonQuant$abundance,
    designMatrix         = myDesign,
    isoformExonAnnoation = system.file("extdata/example.gtf.gz", package="IsoformSwitchAnalyzeR")
)
names(aSwitchList)

### Remove annotation data
aSwitchList <- removeAnnoationData(aSwitchList)
names(aSwitchList)

[Package IsoformSwitchAnalyzeR version 1.4.0 Index]