Bioconductor Git-SVN Bridge authored on 31/08/2014 21:28:19
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+normalize.quantiles.determine.target <- function(x,target.length=NULL,subset=NULL){
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+ |
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+ if (!is.matrix(x)){
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+ stop("This function expects supplied argument to be matrix")
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+ } |
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+ if (!is.numeric(x)){
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+ stop("Supplied argument should be a numeric matrix")
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+ } |
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+ rows <- dim(x)[1] |
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+ cols <- dim(x)[2] |
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+ |
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+ if (is.integer(x)){
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+ x <- matrix(as.double(x), rows, cols) |
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+ } |
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+ |
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+ if (is.null(target.length)){
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+ target.length <- rows |
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+ } |
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+ |
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+ if (target.length <= 0){
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+ stop("Need positive length for target.length")
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+ } |
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+ |
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+ if (is.null(subset)){
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+ return(.Call("R_qnorm_determine_target",x,target.length,PACKAGE="preprocessCore"))
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+ } else {
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+ if (length(subset) != rows){
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+ stop("subset should have same length as nrows(x)")
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+ } |
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+ subset <- as.integer(subset) |
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+ return(.Call("R_qnorm_determine_target_via_subset",x, subset,target.length,PACKAGE="preprocessCore"))
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+ } |
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+ |
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+} |
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+ |
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+ |
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+ |
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+normalize.quantiles.use.target <- function(x,target,copy=TRUE,subset=NULL){
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+ |
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+ if (!is.matrix(x)){
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+ stop("This function expects supplied argument to be matrix")
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+ } |
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+ if (!is.numeric(x)){
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+ stop("Supplied argument should be a numeric matrix")
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+ } |
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+ rows <- dim(x)[1] |
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+ cols <- dim(x)[2] |
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+ |
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+ if (is.integer(x)){
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+ x <- matrix(as.double(x), rows, cols) |
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+ } |
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+ |
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+ if (!is.vector(target)){
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+ stop("This function expects target to be vector")
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+ } |
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+ if (!is.numeric(target)){
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+ stop("Supplied target argument should be a numeric vector")
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+ } |
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+ |
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+ if (is.integer(target)){
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+ target <- as.double(target) |
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+ } |
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+ if (is.null(subset)){
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+ return(.Call("R_qnorm_using_target",x,target,copy,PACKAGE="preprocessCore"))
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+ } else {
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+ if (length(subset) != rows){
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+ stop("subset should have same length as nrows(x)")
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+ } |
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+ subset <- as.integer(subset) |
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+ return(.Call("R_qnorm_using_target_via_subset",x, subset, target, copy, PACKAGE="preprocessCore"))
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+ } |
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+ |
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+ |
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+} |
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+ |
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+ |
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+ |
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+normalize.quantiles.in.blocks <- function(x,blocks,copy=TRUE){
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+ |
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+ rows <- dim(x)[1] |
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+ cols <- dim(x)[2] |
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+ |
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+ if (rows != length(blocks)){
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+ stop("blocks is not vector of correct length")
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+ } |
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+ |
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+ if (is.factor(blocks)){
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+ blocks <- as.integer(blocks) |
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+ } |
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+ |
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+ if (!is.numeric(blocks)){
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+ stop("non-numeric vector used for blocks")
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+ } |
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+ |
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+ |
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+ return(.Call("R_qnorm_within_blocks",x,blocks,copy,PACKAGE="preprocessCore"))
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+ |
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+ |
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+ |
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+} |
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+ |
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+ |
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+ |
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+ |