A function to get the count file for **chromVAR**.

A function to get the count file for **chromVAR**.

getCount(
  sample_list,
  cut_path,
  peak_path,
  peak_suffix = "_peaks_unique.narrowPeak.bed",
  save_file_path = NA
)

Arguments

sample_list

Input a vector containing the names of the samples.

cut_path

The cuts directory obtained by running snakmake.

peak_path

The cuts directory obtained by running snakmake.

peak_suffix

The suffix of the peaks. Default: "_peaks_unique.narrowPeak.bed".

save_file_path

The path to save files.

Examples

  getCount(sample_list=c("s1","s2","s3","s4"), cut_path = "~/snakemake/cuts/", peak_path = "~/snakemake/peaks/", save_file_path = "~/count")
#> Warning: cannot open file 'C:/Users/PC/Documents/snakemake/peaks//s1_peaks_unique.narrowPeak.bed': No such file or directory
#> Error in file(file, "rt"): cannot open the connection