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#' Internal function to normalize mx_dataset using ComBat
#'
#' @param mx_data `mx_dataset` object to normalize
#' @param remove_zeroes,tol,... optional additional arguments for `normalize_mx_combat`
#'
#' @return `mx_dataset` object with normalized data with updated attribute `norm_data` (data.frame) and new attribute `method` (character)
#' @noRd
normalize_mx_combat <- function(mx_data,
remove_zeroes=FALSE,
tol=0.0001,
...){
ndat = mx_data$norm_data
cols = mx_data$marker_cols
slide = mx_data$slide_id
## apply combat function over columns
ndat[,cols] <- sapply(X = cols, function(x){
run_combat(marker=x,
slide_var=slide,
ndat=ndat,
remove_zeroes=remove_zeroes,
tol = tol
)
})
mx_data$norm_data = ndat
mx_data
}
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