isoformToGeneExp {IsoformSwitchAnalyzeR}R Documentation

Summarize isoform expression to gene level expression.

Description

This function extract gene expression from isoform expression by for each condition summing the expression of all isoforms belonging to a specific gene.

Usage

isoformToGeneExp(
    isoformRepExpression,
    isoformGeneAnnotation=NULL,
    quiet = FALSE
)

Arguments

isoformRepExpression

A replicate isoform abundace matrix (not log-transformed). The isoform:gene relationship can be provided by either:

  • Having isoformRepExpression contain two additional colmns 'isoform_id' and 'gene_id' indicating which isoforms are a part of which gene

  • Using the isoformGeneAnnotation argument.

Importantly isoformRepExpression must contain isoform ids either as seperate colum called 'isoform_id' or as row.names. The function will figure it out by itself in what combination the annotation is supplied.

isoformGeneAnnotation

A data.frame or GRange with two (meta) collumns: 'isoform_id' and 'gene_id' indicating the relationship between isoforms and parent gene.

quiet

A logic indicating whether to avoid printing progress messages. Default is FALSE

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"))


### Extract gene info
localAnnotaion <- rtracklayer::import(system.file("extdata/example.gtf.gz", package="IsoformSwitchAnalyzeR"))[,c('transcript_id','gene_id')]
colnames(localAnnotaion@elementMetadata)[1] <- 'isoform_id'

### Summarize to gene level
geneRepCount <- isoformToGeneExp(
    isoformRepExpression  = salmonQuant$counts,
    isoformGeneAnnotation = localAnnotaion
)
[Package IsoformSwitchAnalyzeR version 1.6.0 Index]