isoformToIsoformFraction {IsoformSwitchAnalyzeR}R Documentation

Calculate isoform fraction from isoform abundance matrix

Description

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

Usage

isoformToIsoformFraction(
    isoformRepExpression,
    geneRepExpression=NULL,
    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.

geneRepExpression

Optional. A gene replciate abundance matrix. Must contain gene ids either as seperate colum called 'gene_id' or as row.names.

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

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 seperate data.frame to isoformGeneAnnotation. 2) The ids in isoformRepExpression and geneRepExpression can be supplied either as row.names or as seperate colums 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 1.4.0 Index]