filterGeneExpr {InTAD} | R Documentation

## Function to filter gene expression

### 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")

[Package InTAD version 1.14.0 Index]