This function filters peak files by removing peaks in blacklisted regions and in non-standard chromosomes. It also checks that the input list of peakfiles is named. If no names are provided, default file names will be used.
tidy_peakfile(peaklist, blacklist)A named list of peak files as GRanges object.
Objects must be named and listed using list().
e.g. list("name1"=file1, "name2"=file2)
If not named, default names are assigned.
Peakfile specifying blacklisted regions as GRanges object.
list of GRanges object
### Load Data ###
data("encode_H3K27ac") # example peakfile GRanges object
data("CnT_H3K27ac") # example peakfile GRanges object
data("hg19_blacklist") # blacklist region for hg19 genome
### Create Named Peaklist ###
peaklist <- list("encode"=encode_H3K27ac, "CnT"=CnT_H3K27ac)
### Run ###
peaklist_tidy <- tidy_peakfile(peaklist = peaklist,
blacklist = hg19_blacklist)