normalize_counts: Normalizes read counts

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

Normalizes read counts

Description

Normalizes DNase or ATAC-seq read counts by library sizes. It first obtains the total mapped reads from the current sample, and then scales the read counts for the current data to a reference library size.

Usage

normalize_counts(counts, idxstats_file, ref_size = 1e+08)

Arguments

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

Value

A matrix of normalize read counts.

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