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##
## file: subColSummarize.R
##
## Author: B. M. Bolstad <bmb@bmbolstad.com>
##
## History
## Sept 18, 2007 - Initial verison
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## Dec 10, 2007 - add rownames to output
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##
convert.group.labels <- function(group.labels){
if (!is.factor(group.labels))
group.labels <- as.factor(group.labels)
split(0:(length(group.labels) -1),group.labels)
}
subColSummarizeAvgLog <- function(y, group.labels){
if (!is.matrix(y))
stop("argument should be matrix")
if (!is.double(y) & is.numeric(y))
y <- matrix(as.double(y),dim(y)[1],dim(y)[2])
else if (!is.numeric(y))
stop("argument should be numeric matrix")
rowIndexList <- convert.group.labels(group.labels)
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x <- .Call("R_subColSummarize_avg_log", y, rowIndexList, PACKAGE="preprocessCore")
rownames(x) <- names(rowIndexList)
x
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}
subColSummarizeLogAvg <- function(y, group.labels){
if (!is.matrix(y))
stop("argument should be matrix")
if (!is.double(y) & is.numeric(y))
y <- matrix(as.double(y),dim(y)[1],dim(y)[2])
else if (!is.numeric(y))
stop("argument should be numeric matrix")
rowIndexList <- convert.group.labels(group.labels)
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x <- .Call("R_subColSummarize_log_avg", y, rowIndexList, PACKAGE="preprocessCore")
rownames(x) <- names(rowIndexList)
x
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}
subColSummarizeAvg <- function(y, group.labels){
if (!is.matrix(y))
stop("argument should be matrix")
if (!is.double(y) & is.numeric(y))
y <- matrix(as.double(y),dim(y)[1],dim(y)[2])
else if (!is.numeric(y))
stop("argument should be numeric matrix")
rowIndexList <- convert.group.labels(group.labels)
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x <- .Call("R_subColSummarize_avg", y, rowIndexList, PACKAGE="preprocessCore")
rownames(x) <- names(rowIndexList)
x
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}
subColSummarizeBiweightLog <- function(y, group.labels){
if (!is.matrix(y))
stop("argument should be matrix")
if (!is.double(y) & is.numeric(y))
y <- matrix(as.double(y),dim(y)[1],dim(y)[2])
else if (!is.numeric(y))
stop("argument should be numeric matrix")
rowIndexList <- convert.group.labels(group.labels)
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x <- .Call("R_subColSummarize_biweight_log", y, rowIndexList, PACKAGE="preprocessCore")
rownames(x) <- names(rowIndexList)
x
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}
subColSummarizeBiweight <- function(y, group.labels){
if (!is.matrix(y))
stop("argument should be matrix")
if (!is.double(y) & is.numeric(y))
y <- matrix(as.double(y),dim(y)[1],dim(y)[2])
else if (!is.numeric(y))
stop("argument should be numeric matrix")
rowIndexList <- convert.group.labels(group.labels)
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x <- .Call("R_subColSummarize_biweight", y, rowIndexList, PACKAGE="preprocessCore")
rownames(x) <- names(rowIndexList)
x
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}
subColSummarizeMedianLog <- function(y, group.labels){
if (!is.matrix(y))
stop("argument should be matrix")
if (!is.double(y) & is.numeric(y))
y <- matrix(as.double(y),dim(y)[1],dim(y)[2])
else if (!is.numeric(y))
stop("argument should be numeric matrix")
rowIndexList <- convert.group.labels(group.labels)
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x <- .Call("R_subColSummarize_median_log", y, rowIndexList, PACKAGE="preprocessCore")
rownames(x) <- names(rowIndexList)
x
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}
subColSummarizeLogMedian <- function(y, group.labels){
if (!is.matrix(y))
stop("argument should be matrix")
if (!is.double(y) & is.numeric(y))
y <- matrix(as.double(y),dim(y)[1],dim(y)[2])
else if (!is.numeric(y))
stop("argument should be numeric matrix")
rowIndexList <- convert.group.labels(group.labels)
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x <- .Call("R_subColSummarize_log_median", y, rowIndexList, PACKAGE="preprocessCore")
rownames(x) <- names(rowIndexList)
x
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}
subColSummarizeMedian <- function(y, group.labels){
if (!is.matrix(y))
stop("argument should be matrix")
if (!is.double(y) & is.numeric(y))
y <- matrix(as.double(y),dim(y)[1],dim(y)[2])
else if (!is.numeric(y))
stop("argument should be numeric matrix")
rowIndexList <- convert.group.labels(group.labels)
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x <- .Call("R_subColSummarize_median", y, rowIndexList, PACKAGE="preprocessCore")
rownames(x) <- names(rowIndexList)
x
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}
subColSummarizeMedianpolishLog <- function(y, group.labels){
if (!is.matrix(y))
stop("argument should be matrix")
if (!is.double(y) & is.numeric(y))
y <- matrix(as.double(y),dim(y)[1],dim(y)[2])
else if (!is.numeric(y))
stop("argument should be numeric matrix")
rowIndexList <- convert.group.labels(group.labels)
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x <- .Call("R_subColSummarize_medianpolish_log", y, rowIndexList, PACKAGE="preprocessCore")
rownames(x) <- names(rowIndexList)
x
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}
subColSummarizeMedianpolish <- function(y, group.labels){
if (!is.matrix(y))
stop("argument should be matrix")
if (!is.double(y) & is.numeric(y))
y <- matrix(as.double(y),dim(y)[1],dim(y)[2])
else if (!is.numeric(y))
stop("argument should be numeric matrix")
rowIndexList <- convert.group.labels(group.labels)
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x <- .Call("R_subColSummarize_medianpolish", y, rowIndexList, PACKAGE="preprocessCore")
rownames(x) <- names(rowIndexList)
x
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}
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