isoformToGeneExp {IsoformSwitchAnalyzeR} | R Documentation

## Summarize isoform expression to gene level expression.

### Description

Extract a data.frame with (mean) gene expression, isoform expression or Isoform Fraction values for all conditions (columns) from a switchAnalyzeRlist.

### Usage

    isoformToGeneExp(
        isoRepExpWithGeneId,
        showProgress = TRUE,
        quiet = FALSE
    )

### Arguments

`isoRepExpWithGeneId` | A isoform expression matrix which in addition to expression columns contain two colmns 'isoform_id' and 'gene_id' indicating which isoforms are a part of which gene.
`showProgress` | A logic indicating whether to make a progress bar (if TRUE) or not (if FALSE). Default is TRUE.
`quiet` | A logic indicating whether to avoid printing progress messages. Default is FALSE

### Details

This is just specialized function that is a lot faster than general pourpose functions such as ddplyr.

### 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

    ### Construct data needed from example data in cummeRbund package
    ### (The recomended way of analyzing Cufflinks/Cuffdiff datat is via importCufflinksCummeRbund
    ### This is jus an easy way to get some example data ).
    cuffDB <- prepareCuffExample()

    isoRepCount <- repCountMatrix(isoforms(cuffDB))
    isoRepCount$isoform_id <- rownames(isoRepCount)

    ### add gene info
    localAnnotaion <- import(system.file("extdata/chr1_snippet.gtf", package="cummeRbund"))[,c('transcript_id','gene_id')]
    colnames(localAnnotaion@elementMetadata)[1] <- 'isoform_id'

    isoRepCount$gene_id <- localAnnotaion$gene_id[match(
        isoRepCount$isoform_id , localAnnotaion$isoform_id
    )]

    ### Summarize to gene level
    geneRepCount <- isoformToGeneExp(isoRepCount)

[Package IsoformSwitchAnalyzeR version 1.2.0 Index]