spkAll {spkTools} | R Documentation |
A wrapper for the functions contained in the spkTools package, which calls each function.
spkAll(object, label, model=expr~spike+probe+array, fc=NULL, tol=3, xrngs=NULL, yrngs=NULL, cuts=c(.6,.99), potQuantile=.995, gnn=c(25,100,10000), pch=".", output="eps")
object |
a SpikeInExpressionSet object |
label |
a character string to insert into the graphs and tables produced |
model |
model to be passed to spkAnova |
fc |
the fold change for which fold change plots will be produced |
tol |
the number of digits after the decimal point in fc |
xrngs |
ranges for the x-axis of each plot. d=density, s=slope, v=box, m=M vs A |
yrngs |
ranges for the y-axis of each plot. d=density, s=slope, v=box, m=M vs A |
cuts |
quantiles used to make the low, medium, and high bins |
potQuantile |
the desired quantile to compute the probability of being above |
gnn |
a vector of 3 numbers passed to spkGNN: the desired number of true positives, the number of truly expressed genes, and the number of truly unexpressed genes |
pch |
plotting point to be used in spkSlope |
output |
the format in which to save the plots produced. Options are "pdf" and "eps" |
The full complement of plots and tables described in the vignette are created and saved in the current working directory.
Matthew N. McCall
data(affy) spkAll(affy, label="affy", fc=2)