isoformToIsoformFraction: Calculate isoform fraction from isoform abundance matrix

In kvittingseerup/IsoformSwitchAnalyzeR: Identify, Annotate and Visualize Isoform Switches with Functional Consequences from both short- and long-read RNA-seq data

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
)

kvittingseerup/IsoformSwitchAnalyzeR documentation built on Jan. 14, 2024, 11:30 p.m.