NDC: Normalized Differntial Coverage

In rayanramin/RamPack: Ramin's Package

Normalized Differntial Coverage

Description

NDC1 is the original version that uses the whole genome for normalization ; NDC2 divide the genome into smaller parts for normalization ; NDC3 is similar to NDC2 but better for when coverage is 0 at many positions.

default values are optimized based on e.coli experiments

Usage

NDC(x, y, w = 1e+05, b = 10000, mavn = 120, NDC_Version = 2)

Arguments

x	coverage vector from the treatment sample
y	coverage vector from the control sample
w	width of normalization window (for NDC2|3); w=1e5
b	step size of w; b =1e4
mavn	size of moving average window; mavn = 120
NDC_Version	is the version of NDC; NDC_Version = 2

Examples

NDC(treatment$cov , control$cov , w=5e5 , b = 2e4 , mavn = 150 ) -> NDC

rayanramin/RamPack documentation built on Sept. 2, 2023, 1:20 a.m.