isoformToIsoformFraction {IsoformSwitchAnalyzeR} | R Documentation

## Calculate isoform fraction from isoform abundance matrix

### Description

General purpose function to calculate isoform fraction (IF) matrix from isoform abundance (and potentially gene abundance) matrix.

### Usage

    isoformToIsoformFraction(
        isoformRepExpression,
        geneRepExpression=NULL,
        isoformGeneAnnotation=NULL,
        quiet = FALSE
    )

### Arguments

`isoformRepExpression` | A replicate isoform abundance matrix (not log-transformed) with genes as rows and samples as columns. The isoform:gene relationship can be provided by either: Having `isoformRepExpression` contain two additional columns '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 separate column called 'isoform_id' or as row.names. The function will figure it out by itself in what combination the annotation is supplied.
`geneRepExpression` | Optional. A gene replicate abundance matrix. Must contain gene ids either as separate column called 'gene_id' or as row.names.
`isoformGeneAnnotation` | A data.frame or GRange with two (meta) columns: '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

### Details

This function calculates isoform fractions from isoform abundances. If `geneRepExpression` is not supplied the function automatically calculate it by itself.

Note that: 1) isoform:gene relationship can be supplied as two columns either in the `isoformRepExpression` or as a separate data.frame to `isoformGeneAnnotation`. 2) The ids in `isoformRepExpression` and `geneRepExpression` can be supplied either as row.names or as separate columns respectively called 'isoform_id' and 'gene_id'.

### Value

A replicate isoform fraction matrix with layout similar to `isoformRepExpression`

### 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'

    ### Calculate isoform fractions
    repIF <- isoformToIsoformFraction(
        isoformRepExpression  = salmonQuant$abundance,
        isoformGeneAnnotation = localAnnotaion
    )

[Package IsoformSwitchAnalyzeR version 1.9.1 Index]