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Allow further arguments in msqrobAggregate #61

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Allow further arguments in msqrobAggregate #61

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b1c7cf3
Allow further arguments in msqrobAggregate
StijnVandenbulcke May 7, 2024
cd257e7
added description for ... argument
StijnVandenbulcke May 13, 2024
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18 changes: 12 additions & 6 deletions R/msqrobAggregate.R
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Original file line number Diff line number Diff line change
Expand Up @@ -55,7 +55,9 @@
#' @param aggregateFun A function used for quantitative feature aggregation.
#' Details can be found in the documentation of the `aggregateFeatures`
#' of the `QFeatures` package.
#'
#'
#' @param ... Additional arguments passed to the function specified in the `aggregateFun` argument.
#'
#' @param modelColumnName `character` to indicate the variable name that is used
#' to store the msqrob models in the rowData of the SummarizedExperiment
#' instance or of the assay of the QFeatures instance. Default is "msqrobModels".
Expand Down Expand Up @@ -109,7 +111,8 @@ setMethod(
maxitRob = 1,
tol = 1e-6,
doQR = TRUE,
lmerArgs = list(control = lmerControl(calc.derivs = FALSE))) {
lmerArgs = list(control = lmerControl(calc.derivs = FALSE)),
...) {
if (!fcol %in% colnames(rowData(object)))
stop("The rowData does not contain variable '", fcol, "'.")
if (ridge == FALSE & is.null(findbars(formula)) ){
Expand Down Expand Up @@ -157,7 +160,8 @@ setMethod(
object <- QFeatures::aggregateFeatures(
object = object,
fcol = fcol,
fun = aggregateFun
fun = aggregateFun,
...
)

rowData(object)[[modelColumnName]] <- modelOutput
Expand All @@ -181,7 +185,8 @@ setMethod(
maxitRob = 1,
tol = 1e-6,
doQR = TRUE,
lmerArgs = list(control = lmerControl(calc.derivs = FALSE))) {
lmerArgs = list(control = lmerControl(calc.derivs = FALSE)),
...) {
if (is.null(object[[i]])) stop("QFeatures object does not contain assay ", i)
x <- getWithColData(object, i)
x <- msqrobAggregate(
Expand All @@ -195,9 +200,10 @@ setMethod(
maxitRob = maxitRob,
tol = tol,
doQR = doQR,
lmerArgs = lmerArgs
lmerArgs = lmerArgs,
...
)
object <- addAssay(object, x, name)
addAssayLink(object, i, name, varFrom = fcol, varTo = fcol)
}
)
)
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