setContaminationFraction function

Manually set contamination fraction

Manually set contamination fraction

Manually specify the contamination fraction.

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.

Returns

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)