merge_normalize_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 merged counts.

Description

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

Usage

merge_normalize_counts(counts_files, idxstats_files, ref_size = 1e+08)

Arguments

counts_files	DNase or ATAC-seq read counts matrix files.
idxstats_files	The idxstats files generated by samtools.
ref_size	Scales to reference library size. (Default: 1e8 for DNase-seq and 5e7 for ATAC-seq).

Value

A matrix of merged and normalized counts.

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