tpm.on.subset: Calculate TPM for a subsetted DGEobj

In DGEobj.utils: Differential Gene Expression (DGE) Analysis Utility Toolkit

Calculate TPM for a subsetted DGEobj

Description

Calculates TPM for a heavily subsetted DGEobj. The function will calculate TPM using the original data but returns a DGEobj with the subset.

Usage

tpm.on.subset(dgeObj, applyFilter = TRUE)

Arguments

dgeObj	A DGEobj data structure
applyFilter	Default = TRUE. If TRUE, reduces to the filtered gene list. FALSE returns all genes in the raw data.

Details

TPM should be calculated on a full dataset with only low signal genes removed. tpm.on.subset therefore allows calculation of TPM after heavy filtering of a DGEobj.

Internally, convertCounts uses edgeR's fpkm() to calculate FPKM and converts to TPM using the formula provided by [Harold Pimental](https://haroldpimentel.wordpress.com/2014/05/08/what-the-fpkm-a-review-rna-seq-expression-units/).

Value

A matrix of TPM values

Examples

## Not run: 
   # NOTE: Requires the edgeR package

   dgeObj <- readRDS(system.file("exampleObj.RDS", package = "DGEobj"))
   tpm    <- tpm.on.subset(dgeObj)

## End(Not run)

DGEobj.utils documentation built on May 20, 2022, 1:08 a.m.