The CAFE datalist to be analyzed, i.e. the output of
ProcessCels.
chromNum
The chromosome to be calculated. This can be "ALL"
to calculate all chromosomes.
samples
A vector containing sample numbers to be analyzed
select
Signifies which type of sample selection prompt will be shown, if
samples=NULL. Currently supported are "cli" for a command line
interface and "gui" for a tcl/tk-based graphical user interface.
test
Signifies which statistical test to be used in the final calculation. Must be
either "fisher" for an exact fisher test or "chisqr" for a
chi square test.
bonferroni
If bonferroni=TRUE, will correct the p-values of the enrichment test
with a bonferroni method.
enrichment
Test for over or underexpression. Can be set to "greater" or
"less".
Value
A named vector containing p-values if testing a single chromosome. If
chromNum="ALL", the output will be a two-column data frame, with
cytoband names in the first column and p-values in the second column.