Usage
runQC(arrayData, rnaDeg = TRUE, nuseRle = TRUE, hist = TRUE, boxplot = TRUE, pca = TRUE, colorFactor = 1, colors = c("red", "green", "blue", "yellow", "orange", "purple", "tan", "cyan", "gray60", "black", "white"), save = FALSE, verbose = TRUE)
Arguments
arrayData
an object of class ArrayData
.
rnaDeg
should RNA degradation be detected? Defaults to TRUE
.
nuseRle
should Normalized Unscaled Standard Errors (NUSE) and Relative Log Expressions
(RLE) be calculated? Defaults to TRUE
.
hist
produce histograms of expression values? Defaults to TRUE
.
boxplot
produce boxplots of expression values? Defaults to TRUE
.
pca
should PCA be run? Defaults to TRUE
.
colorFactor
a number specifying which column of the setup (given by the ArrayData
object) should be used for coloring information for the PCA. Defaults to 1.
colors
a character vector of colors to be used in the PCA plot.
save
should the figures be saved? Defaults to FALSE
.
verbose
verbose? Defaults to TRUE
.