get_negconruv: Get Negative and Positive Controls

In YosefLab/scone: Single Cell Overview of Normalized Expression data

Get Negative and Positive Controls

Description

Get Negative and Positive Controls

Usage

get_negconruv(x)

get_negconeval(x)

get_poscon(x)

## S4 method for signature 'SconeExperiment'
get_negconruv(x)

## S4 method for signature 'SconeExperiment'
get_negconeval(x)

## S4 method for signature 'SconeExperiment'
get_poscon(x)

Arguments

x	an object of class SconeExperiment.

Value

NULL or a logical vector.

For get_negconruv the returned vector indicates which genes are negative controls to be used for RUV.

For get_negconeval the returned vector indicates which genes are negative controls to be used for evaluation.

For get_poscon the returned vector indicates which genes are positive controls to be used for evaluation.

Examples

set.seed(42)
mat <- matrix(rpois(500, lambda = 5), ncol=10)
colnames(mat) <- paste("X", 1:ncol(mat), sep="")
obj <- SconeExperiment(mat,negcon_ruv = 1:50 %in% 1:10,
           negcon_eval = 1:50 %in% 11:20,
           poscon = 1:50 %in% 21:30)
negcon_ruv = get_negconruv(obj)
negcon_eval = get_negconeval(obj)
poscon = get_poscon(obj)

YosefLab/scone documentation built on Oct. 21, 2024, 4:39 p.m.