combineWithLoops: Preparation for correlation analysis via loops

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

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

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