bin_transform_counts: Bins and transforms count matrix

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

Bins and transforms count matrix

Description

Bins DNase or ATAC counts using MILLIPEDE binning and then take ‘sqrt’ or ‘log2’ transform

Usage

bin_transform_counts(
  counts,
  bin_method = c("M5", "M24", "M12", "M3", "M2", "M1"),
  transform = c("asinh", "log2", "sqrt", "none")
)

Arguments

counts	DNase or ATAC-seq read counts matrix
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 binned and transformed counts.

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