Assign group names to each file in a named list based on a series of string searches based on combinations of relevant metadata factors.
group_files(peakfiles, searches)A list of peak files as GRanges object and/or as paths to
BED files. If paths are provided, EpiCompare imports the file as GRanges
object. EpiCompare also accepts a list containing a mix of GRanges objects
and paths.Files must be listed and named using list().
E.g. list("name1"=file1, "name2"=file2). If no names are specified,
default file names will be assigned.
A named list of substrings to group peakfiles by.
Named peak files
data("encode_H3K27ac") # example dataset as GRanges object
data("CnT_H3K27ac") # example dataset as GRanges object
data("CnR_H3K27ac") # example dataset as GRanges object
peakfiles <- list(CnR_H3K27ac=CnR_H3K27ac,
CnT_H3K27ac=CnT_H3K27ac,
encode_H3K27ac=encode_H3K27ac)
peaks_grouped <- group_files(peakfiles = peakfiles,
searches=list(assay=c("H3K27ac"),
source=c("Cn","ENCODE")))