CAFE (version 1.8.0)

chromosomeStats: Find aberrations with whole-chromosome resolution

Description

Calculate significant chromosomes with various statistical tests

Usage

chromosomeStats(datalist, chromNum=1, samples=NULL, select="cli", test="fisher",
bonferroni = TRUE, enrichment = "greater")

Arguments

datalist

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.

See Also

bandStats armStats

Examples

data("CAFE_data")
sam <- c(9,11)
chromosomeStats(CAFE_data,chromNum=17,samples=sam,test="fisher")