combineWithLoops {InTAD} | R Documentation

## Preparation for correlation analysis via loops

### Description

This function combines signals and genes based on the usage of loops obtained from HiC data analysis

### Usage

    combineWithLoops(object, loopsInitDf, fragmentLength = 0, tssWidth = 2000,
      extSize = 0)

### Arguments

`object` | InTADSig object
`loopsInitDf` | Data frame with loops. By default 6-column format (chr1,start1,end1,chr2,start2,pos2) is expected.
`fragmentLength` | In case the input format is 4-column (chr1,middlePos1, chr2, middlePos2) fragment length should be provided to extend the corresponding loci for loop start and end positions.
`tssWidth` | The transcription start site width is used to control overlaps with loop anchor. Default is 2000 base pairs.
`extSize` | The loop endings can be extended upstream and downstream with provided corresponding increase size in base pairs.

### Details

The expected input is the loops data.frame applied to find connections of signals to genes. This data.frame could be in two formats: either (chr1,start1,end1,chr2,start2,end2) or (chr1,middlePos1,chr2,middlePos2) with fragment size.

### Value

Updated InTADSig object containing genes connected to signals via loops

[Package InTAD version 1.12.0 Index]