merge_normalize_bin_transform_counts: Merges DNase or ATAC-seq counts from multiple replicates,...

In HarteminkLab/TOP: Predict transcription factor occupancy using DNase- or ATAC-seq data

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

Description

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.

Usage

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.

HarteminkLab/TOP documentation built on July 27, 2023, 6:14 p.m.