Usage
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")
Arguments
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"