Bioconductor Git-SVN Bridge authored on 31/08/2014 21:28:19
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+## |
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+## file: subColSummarize.R |
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+## |
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+## Author: B. M. Bolstad <bmb@bmbolstad.com> |
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+## |
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+## History |
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+## Sept 18, 2007 - Initial verison |
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+## Dec 10, 2007 - add rownames to output |
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+## |
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+ |
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+ |
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+convert.group.labels <- function(group.labels){
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+ |
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+ if (!is.factor(group.labels)) |
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+ group.labels <- as.factor(group.labels) |
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+ |
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+ split(0:(length(group.labels) -1),group.labels) |
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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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+subColSummarizeAvgLog <- function(y, group.labels){
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+ if (!is.matrix(y)) |
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+ stop("argument should be matrix")
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+ |
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+ if (!is.double(y) & is.numeric(y)) |
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+ y <- matrix(as.double(y),dim(y)[1],dim(y)[2]) |
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+ else if (!is.numeric(y)) |
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+ stop("argument should be numeric matrix")
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+ |
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+ rowIndexList <- convert.group.labels(group.labels) |
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+ |
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+ x <- .Call("R_subColSummarize_avg_log", y, rowIndexList, PACKAGE="preprocessCore")
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+ |
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+ rownames(x) <- names(rowIndexList) |
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+ x |
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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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+subColSummarizeLogAvg <- function(y, group.labels){
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+ if (!is.matrix(y)) |
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+ stop("argument should be matrix")
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+ |
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+ if (!is.double(y) & is.numeric(y)) |
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+ y <- matrix(as.double(y),dim(y)[1],dim(y)[2]) |
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+ else if (!is.numeric(y)) |
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+ stop("argument should be numeric matrix")
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+ |
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+ rowIndexList <- convert.group.labels(group.labels) |
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+ |
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+ x <- .Call("R_subColSummarize_log_avg", y, rowIndexList, PACKAGE="preprocessCore")
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+ rownames(x) <- names(rowIndexList) |
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+ x |
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+} |
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+ |
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+ |
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+ |
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+ |
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+subColSummarizeAvg <- function(y, group.labels){
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+ if (!is.matrix(y)) |
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+ stop("argument should be matrix")
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+ |
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+ if (!is.double(y) & is.numeric(y)) |
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+ y <- matrix(as.double(y),dim(y)[1],dim(y)[2]) |
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+ else if (!is.numeric(y)) |
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+ stop("argument should be numeric matrix")
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+ |
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+ rowIndexList <- convert.group.labels(group.labels) |
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+ |
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+ x <- .Call("R_subColSummarize_avg", y, rowIndexList, PACKAGE="preprocessCore")
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+ rownames(x) <- names(rowIndexList) |
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+ x |
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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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+subColSummarizeBiweightLog <- function(y, group.labels){
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+ if (!is.matrix(y)) |
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+ stop("argument should be matrix")
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+ |
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+ if (!is.double(y) & is.numeric(y)) |
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+ y <- matrix(as.double(y),dim(y)[1],dim(y)[2]) |
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+ else if (!is.numeric(y)) |
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+ stop("argument should be numeric matrix")
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+ |
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+ rowIndexList <- convert.group.labels(group.labels) |
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+ |
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+ x <- .Call("R_subColSummarize_biweight_log", y, rowIndexList, PACKAGE="preprocessCore")
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+ rownames(x) <- names(rowIndexList) |
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+ x |
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+} |
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+ |
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+ |
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+ |
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+ |
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+subColSummarizeBiweight <- function(y, group.labels){
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+ if (!is.matrix(y)) |
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+ stop("argument should be matrix")
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+ |
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+ if (!is.double(y) & is.numeric(y)) |
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+ y <- matrix(as.double(y),dim(y)[1],dim(y)[2]) |
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+ else if (!is.numeric(y)) |
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+ stop("argument should be numeric matrix")
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+ |
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+ rowIndexList <- convert.group.labels(group.labels) |
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+ |
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+ x <- .Call("R_subColSummarize_biweight", y, rowIndexList, PACKAGE="preprocessCore")
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+ rownames(x) <- names(rowIndexList) |
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+ x |
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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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+ |
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+subColSummarizeMedianLog <- function(y, group.labels){
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+ if (!is.matrix(y)) |
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+ stop("argument should be matrix")
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+ |
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+ if (!is.double(y) & is.numeric(y)) |
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+ y <- matrix(as.double(y),dim(y)[1],dim(y)[2]) |
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+ else if (!is.numeric(y)) |
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+ stop("argument should be numeric matrix")
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+ |
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+ rowIndexList <- convert.group.labels(group.labels) |
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+ |
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+ x <- .Call("R_subColSummarize_median_log", y, rowIndexList, PACKAGE="preprocessCore")
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+ rownames(x) <- names(rowIndexList) |
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+ x |
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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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+subColSummarizeLogMedian <- function(y, group.labels){
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+ if (!is.matrix(y)) |
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+ stop("argument should be matrix")
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+ |
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+ if (!is.double(y) & is.numeric(y)) |
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+ y <- matrix(as.double(y),dim(y)[1],dim(y)[2]) |
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+ else if (!is.numeric(y)) |
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+ stop("argument should be numeric matrix")
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+ |
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+ rowIndexList <- convert.group.labels(group.labels) |
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+ |
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+ x <- .Call("R_subColSummarize_log_median", y, rowIndexList, PACKAGE="preprocessCore")
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+ rownames(x) <- names(rowIndexList) |
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+ x |
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+} |
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+ |
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+ |
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+ |
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+ |
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+subColSummarizeMedian <- function(y, group.labels){
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+ if (!is.matrix(y)) |
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+ stop("argument should be matrix")
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+ |
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+ if (!is.double(y) & is.numeric(y)) |
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+ y <- matrix(as.double(y),dim(y)[1],dim(y)[2]) |
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+ else if (!is.numeric(y)) |
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+ stop("argument should be numeric matrix")
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+ |
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+ rowIndexList <- convert.group.labels(group.labels) |
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+ |
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+ x <- .Call("R_subColSummarize_median", y, rowIndexList, PACKAGE="preprocessCore")
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+ rownames(x) <- names(rowIndexList) |
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+ x |
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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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+ |
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+subColSummarizeMedianpolishLog <- function(y, group.labels){
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+ if (!is.matrix(y)) |
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+ stop("argument should be matrix")
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+ |
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+ if (!is.double(y) & is.numeric(y)) |
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+ y <- matrix(as.double(y),dim(y)[1],dim(y)[2]) |
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+ else if (!is.numeric(y)) |
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+ stop("argument should be numeric matrix")
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+ |
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+ rowIndexList <- convert.group.labels(group.labels) |
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+ |
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+ x <- .Call("R_subColSummarize_medianpolish_log", y, rowIndexList, PACKAGE="preprocessCore")
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+ rownames(x) <- names(rowIndexList) |
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+ x |
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+} |
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+ |
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+ |
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+subColSummarizeMedianpolish <- function(y, group.labels){
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+ if (!is.matrix(y)) |
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+ stop("argument should be matrix")
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+ |
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+ if (!is.double(y) & is.numeric(y)) |
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+ y <- matrix(as.double(y),dim(y)[1],dim(y)[2]) |
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+ else if (!is.numeric(y)) |
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+ stop("argument should be numeric matrix")
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+ |
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+ rowIndexList <- convert.group.labels(group.labels) |
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+ |
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+ x <- .Call("R_subColSummarize_medianpolish", y, rowIndexList, PACKAGE="preprocessCore")
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+ rownames(x) <- names(rowIndexList) |
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+ x |
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+} |
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+ |