add_in_silico_root: build an in-silico root cell and clone profile

In SingerLab/gac: Genetic Analysis of Cells

build an in-silico root cell and clone profile

Description

By default cell is a female diploid cell

Usage

add_in_silico_root(cnr, base.ploidy = 2L, cell.name = "diploid", female = TRUE)

Arguments

cnr	a cnr
base.ploidy	integer, base ploidy (2, 4, 6, 8), default 2, for diploid cell
cell.name	name of root cell. default "diploid"
female	logical, weather to build a female or male cell and clone, default is female. If female is NULL, no sex chromosomes correction is performed, all bins will have copy number equal base.ploidy

Value

Append an in-silico diplod (or polyploid) cell to the cnr. By default a female human genome is created. If FALSE, a male human genome is constructed. NULL will not peform a gender correction and the entire genome will be set to the base ploidy.

In tetraploid males copy number is half of the base.ploidy e.g. for 4n : X = 2, Y = 2.

Examples

data(cnr)

cnr <- add_in_silico_root(cnr)

head(cnr$Y)

SingerLab/gac documentation built on March 23, 2024, 5:15 a.m.