getNormalizationMatrix: Get normalization matrix

In UMI4Cats: UMI4Cats: Processing, analysis and visualization of UMI-4C chromatin contact data

Description

Will return a normalization matrix.

Usage

getNormalizationMatrix(
  umi4c,
  norm_bins = 10^(3:6),
  post_smooth_win = 50,
  r_expand = 1.2
)

Arguments

umi4c	UMI4C object as generated by makeUMI4C.
norm_bins	Numeric vector with the genomic bins to use for normalization. Default: 1K, 10K, 100K, 1Mb.
post_smooth_win	Numeric indicating the smoothing window to use. Default: 50.
r_expand	Numeric indicanting the expansion value for normalization. Default: 1.2.

Value

Creates a matrix of normalization factors using as a reference the profile specified in the UMI4C object.

UMI4Cats documentation built on Dec. 31, 2020, 2:01 a.m.