RLE_NUSE: Make relative log expression values (RLE) and normalized...

In machalen/QualityGraphs: Make quality graphs for microarray data based on objects obtained witharoma affymetrix normalization.

Usage

RLE_NUSE(bpstats, kind, strt = NULL, nd = NULL, parameters, lab, conditions = NULL, colors = NULL)

Arguments

bpstats
kind
strt
nd
parameters
lab
conditions
colors

Examples

##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--	or do  help(data=index)  for the standard data sets.

## The function is currently defined as
function (bpstats, kind, strt = NULL, nd = NULL, parameters, 
    lab, conditions = NULL, colors = NULL) 
{
    if (is.null(labels)) {
        labels <- gsub(paste("_(", xip, ")", sep = ""), "", ds$Names, 
            fixed = TRUE)
    }
    if (is.null(strt) & is.null(nd)) {
        strt <- 1
        nd <- length(bpstats)
    }
    else if (is.null(strt)) {
        strt <- 1
    }
    else if (is.null(nd)) {
        nd <- length(bpstats)
    }
    fitxer_int <- as.list(1:nd)
    for (i in (strt:nd)) {
        fitxer_int[[i]] <- bpstats[[i]]$stats
    }
    if (is.null(conditions)) {
        boxplot(fitxer_int[strt:nd], main = paste(kind, "plot"), 
            xaxt = "n")
        axis(1, at = 1:length(lab), labels = lab, cex.axis = parameters$ce, 
            las = 2)
    }
    else if (is.null(colors)) {
        CondNames <- mixedsort(lab)
        CondTable <- data.frame(CondNames, conditions)
        conditions.o <- CondTable[match(lab, CondTable$CondNames), 
            "conditions"]
        list1 <- unique(as.character(sort(conditions.o)))
        ColVect <- c(brewer.pal(8, "Dark2"), brewer.pal(12, "Paired"))
        list2 <- ColVect[1:length(unique(conditions.o))]
        map = setNames(list2, list1)
        colors <- map[conditions.o]
        boxplot(fitxer_int[strt:nd], main = paste(kind, "plot"), 
            xaxt = "n", col = colors)
        axis(1, at = 1:length(lab), labels = lab, cex.axis = parameters$ce, 
            las = 2)
        legend("topright", legend = list1, cex = parameters$ce + 
            0.2, fill = list2)
    }
    else {
        CondNames <- mixedsort(lab)
        CondTable <- data.frame(CondNames, conditions)
        conditions.o <- CondTable[match(lab, CondTable$CondNames), 
            "conditions"]
        list1 <- unique(conditions.o)
        list2 <- colors
        map = setNames(list2, list1)
        colors <- map[conditions.o]
        boxplot(fitxer_int[strt:nd], main = paste(kind, "plot"), 
            xaxt = "n", col = colors)
        axis(1, at = 1:length(lab), labels = lab, cex.axis = parameters$ce, 
            las = 2)
        legend("topright", legend = list1, cex = parameters$ce + 
            0.2, fill = list2)
    }
  }

machalen/QualityGraphs documentation built on Oct. 22, 2019, 8:29 p.m.