Merges DNase or ATAC-seq counts from multiple replicates, then normalizes, bin and transform the merged counts

Merges DNase-seq or ATAC-seq read counts from multiple replicate samples, normalizes the read counts by scaling to the reference library size, then bins and transforms the merged counts.

merge_normalize_bin_transform_counts(
  counts_files,
  idxstats_files,
  ref_size = 1e+08,
  bin_method = c("M5", "M24", "M12", "M3", "M2", "M1"),
  transform = c("asinh", "log2", "sqrt", "none")
)

Arguments

counts_files

DNase or ATAC-seq read counts matrix files.

idxstats_files

The idxstats files generated by samtools.

ref_size

Scale to DNase-seq or ATAC-seq reference library size. (Default: 1e8 for DNase-seq and 5e7 for ATAC-seq).

bin_method

MILLIPEDE binning scheme (default: ‘M5’).

transform

Type of transformation for DNase or ATAC counts. Options: ‘asinh’, ‘log2’, ‘sqrt’, ‘none’.

Value

A data frame of merged, normalized, binned, and transformed counts.