vennCounts2 {affycoretools} | R Documentation |
This function is designed to compute counts for a Venn diagram. It is
slightly different from vennCounts
in the
additional ability to compute counts for genes that are differentially
expressed in the same direction.
vennCounts2(x, method = "same", fit = NULL, foldFilt = NULL)
x |
A TestResults object, produced by a
call to decideTests or foldFilt . |
method |
One of "same", "both", "up", "down". See details for more information. |
fit |
An MArrayLM object, produced by a call
to lmFit and eBayes . Only
necessary if 'foldFilt' = TRUE . |
foldFilt |
A fold change to filter samples. This is primarily
here for consistency with the corresponding argument in
vennSelect . |
The function vennCounts
will return identical
results except for the "same" method. This will only select those
genes that both pass the criteria of decideTests
as well as being differentially expressed in the same direction. Note
that this is different from the "both" method, which simply requires
that a given gene be differentially expressed in e.g., two different
comparisons without any requirement that the direction be the same.
A VennCounts
object.
James W. MacDonald <jmacdon@med.umich.edu>
tstat <- matrix(rt(300,df=10),100,3) tstat[1:33,] <- tstat[1:33,]+2 clas <- classifyTestsF(tstat,df=10,p.value=0.05) a <- vennCounts2(clas) print(a) vennDiagram(a)