sortedIqrPlot {ffpe} | R Documentation |
This plots only the 25th to 75th percentile of expression intensities (Interquartile Range), sorted from smallest to largest IQR. This modification is more readable than a regular boxplot for large sample sizes. An optional batch variable may be specified, so that the sorting is done within each batch.
sortedIqrPlot(data.obj, batchvar = rep(1, ncol(data.obj)), dolog2=FALSE, ...) ## S4 method for signature 'LumiBatch' sortedIqrPlot(data.obj, batchvar = rep(1, ncol(data.obj)), dolog2=FALSE, ...) ## S4 method for signature 'AffyBatch' sortedIqrPlot(data.obj, batchvar = rep(1, ncol(data.obj)), dolog2=FALSE, ...) ## S4 method for signature 'matrix' sortedIqrPlot(data.obj, batchvar = rep(1, ncol(data.obj)), dolog2=FALSE, ...)
data.obj |
An object of class LumiBatch, AffyBatch, AffyBatch, or matrix. This should contain raw, unnormalized, expression intensities. |
batchvar |
Optional integer batch variable. If specified, samples will be sorted within batches only. Default is to assume a single batch for all data. |
dolog2 |
If TRUE, data will be log2-transformed before plotting. Default is FALSE. |
... |
Optional arguments passed on to the plot() function. |
Function will be generally called for the side-effect of producing a plot of sorted IQRs, but if the output is redirected it also produces the IQRs.
If the output is redirected, e.g.:
output <- sortedIqrPlot()
the function will return the IQR of each sample.
Levi Waldron <lwaldron@hsph.harvard.edu>
Under review.
sampleQC
library(ffpeExampleData) data(lumibatch.GSE17565) sortedIqrPlot(lumibatch.GSE17565,main="GSE17565")