Bioconductor Git-SVN Bridge authored on 31/08/2014 21:28:19
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+rcModelPLM <- function(y,row.effects=NULL, input.scale=NULL){
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+ if (!is.matrix(y)) |
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+ stop("argument should be matrix")
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+ PsiCode <- 0 |
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+ PsiK <- 1.345 |
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+ if (is.null(row.effects)){
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+ .Call("R_rlm_rma_default_model",y,PsiCode,PsiK,input.scale,PACKAGE="preprocessCore")
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+ } else {
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+ if (length(row.effects) != nrow(y)){
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+ stop("row.effects parameter should be same length as number of rows")
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+ } |
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+ if (abs(sum(row.effects)) > length(row.effects)*.Machine$double.eps){
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+ stop("row.effects should sum to zero")
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+ } |
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+ .Call("R_rlm_rma_given_probe_effects",y,as.double(row.effects),PsiCode,PsiK,input.scale,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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+rcModelWPLM <- function(y, w, row.effects=NULL, input.scale=NULL){
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+ if (!is.matrix(y)) |
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+ stop("argument should be matrix")
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+ if (is.vector(w)){
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+ if (length(w) != prod(dim(y))){
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+ stop("weights are not correct length")
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+ } |
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+ } else if (is.matrix(w)){
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+ if (!all(dim(w) == dim(y))){
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+ stop("weights should be same dimension as input matrix")
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+ } |
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+ |
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+ } |
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+ if (any(w < 0)){
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+ stop("weights should be no negative")
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+ } |
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+ |
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+ |
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+ |
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+ PsiCode <- 0 |
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+ PsiK <- 1.345 |
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+ if (is.null(row.effects)){
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+ .Call("R_wrlm_rma_default_model",y,PsiCode,PsiK,as.double(w),input.scale,PACKAGE="preprocessCore")
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+ } else {
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+ if (length(row.effects) != nrow(y)){
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+ stop("row.effects parameter should be same length as number of rows")
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+ } |
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+ if (abs(sum(row.effects)) > length(row.effects)*.Machine$double.eps){
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+ stop("row.effects should sum to zero")
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+ } |
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+ .Call("R_wrlm_rma_given_probe_effects",y,as.double(row.effects),PsiCode,PsiK,as.double(w),input.scale,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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+rcModelMedianPolish <- function(y){
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+ if (!is.matrix(y)) |
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+ stop("argument should be matrix")
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+ PsiCode <- 0 |
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+ PsiK <- 1.345 |
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+ .Call("R_medianpolish_rma_default_model",y,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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+subrcModelMedianPolish <- function(y,group.labels){
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+ |
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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_sub_rcModelSummarize_medianpolish", y, rowIndexList,PACKAGE="preprocessCore")
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+ |
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+ names(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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+subrcModelPLM <- function(y,group.labels,row.effects=NULL, input.scale=NULL){
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+ |
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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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+ PsiCode <- 0 |
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+ PsiK <- 1.345 |
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+ |
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+ if (is.null(row.effects)){
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+ x <- .Call("R_sub_rcModelSummarize_plm", y, rowIndexList, PsiCode, PsiK, input.scale,PACKAGE="preprocessCore")
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+ names(x) <- names(rowIndexList) |
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+ x |
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+ |
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+ } else {
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+ stop("row.effects not yet implemented for subrcModelPLM")
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+ if (length(row.effects) != nrow(y)){
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+ stop("row.effects parameter should be same length as number of rows")
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+ } |
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+ if (abs(sum(row.effects)) > 10*.Machine$double.eps){
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+ stop("row.effects should sum to zero")
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+ } |
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+ .Call("R_rlm_rma_given_probe_effects",y,as.double(row.effects),PsiCode,PsiK,input.scale,PACKAGE="preprocessCore")
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+ } |
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+} |
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+ |