makeAx4TPM: makeAx4TPM

In WilliamSalvidge/dictyChipSeq: What the Package Does (One Line, Title Case)

makeAx4TPM

Description

TPM (Transcript per Million) normalisation of Ax4 RNA-Seq data. Returns Genes and norm expression for those genes with above zero readcount. TPM normalises gene expression with gene length included. See StatQuest RPKM FPKM and TPM Clearly Explained on YouTube for good explanation.

Usage

makeAx4TPM(x)

Arguments

x	should be a 6 column un-normalised ax4 set1 readcounts file. Can be found in the dicty_chip_seq Rproj or in RNA-Seq folder in Dropbox

Details

This could maybe be split into two functions one which gets the width of genes from the dicty TxDb object another which actually does the TPM calculation

Extra info: Bioconductor Forum Page Mike Love guy who created DESEq2. All columns now = 1e6 as he says it should

Value

TPM matrix

WilliamSalvidge/dictyChipSeq documentation built on March 28, 2023, 1:27 a.m.