filterGeneExpr: Function to filter gene expression

Description Usage Arguments Details Value Examples

View source: R/filterGeneExpr.R

Description

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

Usage

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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

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## 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")

InTAD documentation built on Dec. 7, 2018, 6 p.m.