setContaminationFraction: Manually set contamination fraction

In SoupX: Single Cell mRNA Soup eXterminator

Manually set contamination fraction

Description

Manually specify the contamination fraction.

Usage

setContaminationFraction(sc, contFrac, forceAccept = FALSE)

Arguments

sc	A SoupChannel object.
contFrac	The contamination fraction. Either a constant, in which case the same value is used for all cells, or a named vector, in which case the value is set for each cell.
forceAccept	A warning or error is usually returned for extremely high contamination fractions. Setting this to TRUE will turn these into messages and proceed.

Value

A modified SoupChannel object for which the contamination (rho) has been set.

Examples

sc = load10X(system.file('extdata','toyData',package='SoupX'))
sc = setContaminationFraction(sc,0.1)

SoupX documentation built on Nov. 1, 2022, 5:05 p.m.