group_files: Group files

In neurogenomics/EpiCompare: Comparison, Benchmarking & QC of Epigenomic Datasets

Group files

Description

Assign group names to each file in a named list based on a series of string searches based on combinations of relevant metadata factors.

Usage

group_files(peakfiles, searches)

Arguments

peakfiles	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.
searches	A named list of substrings to group peakfiles by.

Value

Named peak files

Examples

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")))

neurogenomics/EpiCompare documentation built on April 30, 2024, 3:58 p.m.