isoformFrac: Function isoformFrac

In jrthompson54/DGE.Tools2: A function library to facilitate Differential Gene Expression Analysis

Description

Takes a dgeObj as input (transcript level data) and returns a matrix containing isoform fraction data.

Usage

isoformFrac(dgeObj, dataType = "fpkm", normalize = "tmm")

Arguments

dgeObj	An isoform level DGEobj created by function initDGEobj, Xpress2DGEO or OmicsoftToDgeObj. Counts and isoformData must be present in the DGEobj (required). isoformData$ExonLength must be present or assay = "effectiveLength" must be present.
dataType	One of "fpkm" or "tpm" (default="fpkm")
normalize	Default = "TMM" and invokes TMM normalization. Other allowed values are: "RLE","upperquartile", "none". Invokes edgeR::calcNormFactors for normalization. Only invoked when dataType="fpkm". This is because applying TPM essentially erases any prior column scaling so TMM and similar normalizations have no effect.

Details

Isoform Fraction is calculated using length normalized data (FPKM or TPM), as length normalized data is required because different isoforms have different total exon lengths. If FPKM is specified, you can also specify a normalization (via edgeR::calcNormFactors). Isoform fraction is calculated simply as the isoform intensity divided by the summed gene intensity for all isoforms of a given gene.

TPM or FPKM are calculated directly from counts using all data in the dgeObj. I recommend performing low intensity filtering at the gene level before running isoformFrac.

Value

A DGEobj with an isoform fraction dataframe added

Author(s)

John Thompson, [e-mail]

Examples

   MyDgeObj <- isoformFrac(MyDgeObj)

jrthompson54/DGE.Tools2 documentation built on May 12, 2021, 8:47 p.m.