roundCNR: rounded quantal matrix

View source: R/roundCNR.R

roundCNRR Documentation

rounded quantal matrix

Description

Rounds an X matrix to the nearest integer with special threasholds specific to single-cell quantal data from the Varbin algorithm for deletions, losses, and neutral (2 copies)

Usage

roundCNR(X, neut = 2.5, loss = 1.2, del = 0.2)

Arguments

X

a numerical matrix composed of bins with copy numbers estimates integer or numerical

neut

maximum value that will be floored to a neutral copy number for diploid species i.e. 2

loss

lower bound for neutral, and upper bound threshold to be considered a loss of one copy

del

maximum threshold to consider a total deletion of the bin i.e. 0 copies

Value

Rounds X based on quantal

Examples


data(copynumbers)

head(copynumbers)

cni <- roundCNR(copynumbers)

head(cni)


SingerLab/gac documentation built on Oct. 14, 2022, 4:09 a.m.