filterGeneExpr: Function to filter gene expression

In kokonech/InTAD: Search for correlation between epigenetic signals and gene expression in TADs

Description

This function performs filtering of gene expression counts based on various parameters

Usage

filterGeneExpr(obj, cutVal = 0, geneType = NA, checkExprDistr = FALSE,
  plotExprDistr = FALSE)

Arguments

obj	InTADSig object
cutVal	Exclude genes that have max expression less or equal to this value in all samples. Default: 0
geneType	Type of gene to select for filtering i.e. "protein_coding". Default:NA
checkExprDistr	Adjust cutVal based on gene expression distribution
plotExprDistr	Perform visualziation of the distribution

Details

The function allows to stabilize the functional activity of the genes. By default all not expressed genes are filtered. It is also possible to set type of gene to take into account i.e. "protein_coding" only. This option requires additional metadata column "transcript_type". Also, special filtering option based on mclust library allows to analyze distribution of counts and adjust the cut value to exclude low expressed genes.

Value

InTADSig object with filtered counts table

Examples

## perform analysis on test data
inTadSig <- newSigInTAD(enhSel, enhSelGR, rpkmCountsSel, txsSel)
## default filtering
inTadSig <- filterGeneExpr(inTadSig)
## filter based on gene type
inTadSig <- filterGeneExpr(inTadSig, geneType = "protein_coding")

kokonech/InTAD documentation built on Jan. 1, 2021, 9:23 p.m.