combineWithLoops: Preparation for correlation analysis via loops

Description Usage Arguments Details Value

View source: R/combineSignalsWithLoops.R

Description

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

Usage

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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


InTAD documentation built on Nov. 8, 2020, 7:47 p.m.