cal_footprint_cuts: Calculate cuts

In jiang-junyao/IReNA: IReNA

Calculate cuts

Description

Function to calculate cuts of each position in footprints

Usage

cal_footprint_cuts(bamfilepath, bedfile, index_bam = FALSE, workers = NULL)

Arguments

bamfilepath	character, indicating the path of bam file
bedfile	bed file of footprints, generated by get_peaks_genes()
index_bam	logical, indicating whether to index the bam file. If bam file do not have a matched bai file, this parameter should be TRUE
workers	number of cores

Value

return formated wig file

Examples

load(system.file("extdata", "list1.rda", package = "IReNA"))
load(system.file("extdata", "test_clustering.rda", package = "IReNA"))
bamfilepath1<-'mmATACCtrW00R1_CuFiQ10No_sorted.bam'
bamfilepath2<-'mmATACCtrW00R2_CuFiQ10No_sorted.bam'
test_clustering <- add_ENSID(test_clustering, Spec1 = "Hs")
list2<-get_related_peaks(list1,test_clustering)
#cuts1<-cal_footprint_cuts(bamfilepath = bamfilepath1,bedfile = list2[[1]])
#cuts2<-cal_footprint_cuts(bamfilepath = bamfilepath2,bedfile = list2[[1]])
#cuts_list<-list(cuts1,cuts2)

jiang-junyao/IReNA documentation built on Nov. 4, 2024, 8:29 p.m.