combineWithLoops {InTAD} | R Documentation |
This function combines signals and genes based on the usage of loops obtained from HiC data analysis
combineWithLoops(object, loopsInitDf, fragmentLength = 0, tssWidth = 2000, extSize = 0)
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. |
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.
Updated InTADSig object containing genes connected to signals via loops