combineInTAD: Preparation for correlation analysis

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

Description

This function combines signals and genes in inside of Topologically Associated Domains (TADs)

Usage

combineInTAD(object, tadGR, selMaxTadOvlp = TRUE, closestGene = TRUE)

Arguments

object	InTADSig object
tadGR	TAD genomic regions
selMaxTadOvlp	If a signal overlaps 2 or more TADs by default only single TAD with max overlap is selected.All overlaps can be included by deactivating this option.
closestGene	By default closest to TAD genes are selected based on TSS location. Deactivate this option to use genes only lying within TAD.

Details

Each signal is checked if it is lying inside of TAD. Signals out of TADs are ignored. The genomic regions reprenting gene coordiantes are converted to TSS. By default, the closest genes are assigned belonging to TAD. If this option deactivated, only those lying with TAD are collected. Result is a list of signals connected to tables with gene details.

Value

Updated InTADSig object containing genes connected to eash signal

Examples

# create sigInTAD object
inTadSig <- newSigInTAD(enhSel, enhSelGR, rpkmCountsSel, txsSel)
# combine signals and genes in TAD
inTadSig <- combineInTAD(inTadSig, tadGR)

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