normalize_chip: Normalizes (and transforms) ChIP-seq read coverage

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

Normalizes (and transforms) ChIP-seq read coverage

Description

Normalizes the ChIP-seq read counts by scaling to the reference ChIP-seq library size, and transforms the ChIP-seq read counts.

Usage

normalize_chip(
  chip_counts,
  idxstats_file,
  ref_size = 2e+07,
  transform = c("none", "asinh", "log2", "sqrt")
)

Arguments

chip_counts	A vector of ChIP-seq counts.
idxstats_file	The idxstats file generated by samtools.
ref_size	ChIP-Seq reference library size (Default: 20 million).
transform	Type of transformation for the ChIP read counts. Options are ‘none’ (no transformation), ‘asinh’, ‘log2’, and ‘'sqrt'’.

Value

A vector of transformed ChIP-seq counts.

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