runEscape not passing BPPARAM properly

[LinearParadox]

Currently, when you use runEscape the package ignores multiprocess settings. I'm pretty sure this is due to the runEscape function not passing the object to the escape.matrix method.

Currently it is:

function (input.data, gene.sets = NULL, method = "ssGSEA", groups = 1000, 
    min.size = 5, normalize = FALSE, make.positive = FALSE, new.assay.name = "escape", 
    BPPARAM = SerialParam(), ...) 
{
    .checkSingleObject(input.data)
    enrichment <- escape.matrix(input.data = input.data, gene.sets = gene.sets, 
        method = method, groups = groups, min.size = min.size)
    input.data <- .adding.Enrich(input.data, enrichment, new.assay.name)
    return(input.data)
}

It seems to work when modified to:

function (input.data, gene.sets = NULL, method = "ssGSEA", groups = 1000, 
    min.size = 5, normalize = FALSE, make.positive = FALSE, new.assay.name = "escape", 
    BPPARAM = SerialParam(), ...) 
{
    .checkSingleObject(input.data)
    enrichment <- escape.matrix(input.data = input.data, gene.sets = gene.sets, 
        method = method, groups = groups, min.size = min.size, BPPARAM = BPPARAM)
    input.data <- .adding.Enrich(input.data, enrichment, new.assay.name)
    return(input.data)
}

[ncborcherding]

Hey Alexei,

You are totally correct, just commited the fix to the repository and will update bioconductor version soon.