combineInTAD {InTAD} | R Documentation

## Preparation for correlation analysis

### 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)

[Package InTAD version 1.10.0 Index]