loadPeakFile: loadPeakFile

In shangguandong1996/FindIT2: find influential TF and Target based on multi-omics data

loadPeakFile

Description

read peak file and transform it into GRanges object

Usage

loadPeakFile(filePath, TFBS_database = FALSE)

Arguments

filePath	peak Path
TFBS_database	whether your peak file is a TFBS database file. If you want the final GRanges have a column named "TF_id", you should set TFBS_database TRUE. The GRanges with TF_id can be applied in "TF_GR_database" parameter of findIT_TFHit, findIT_enrichFisher, findIT_enrichWilcox, findIT_regionRP. If FALSE, the GRanges will have a column named "feature_id", which always be the input of "peak_GR" parameter.

Details

The GRanges with TF_id always be the input of "TF_GR_database" parameter. It represents the TFBS database like motif scan result, public database ChIP-seq site and so on.

The GRanges with feature_id always be the input of "peak_GR" parameter.

Value

GRanges object with a column named feature_id or TF_id

Examples

peakfile <- system.file("extdata", "ChIP.bed.gz", package = "FindIT2")
loadPeakFile(peakfile)

shangguandong1996/FindIT2 documentation built on March 1, 2024, 8:34 p.m.