get_negconruv {scone} | R Documentation

## 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)

[Package scone version 1.18.0 Index]