CAFE (version 1.8.0)

armStats: Find aberrations with chromosome arm resolution

Description

Calculate significant chromosomal arms with various statistical tests

Usage

armStats(datalist, chromNum=1, arm="q",
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.

arm

Select which arm - "q" or "p" - to analyse

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

chromosomeStats bandStats

Examples

data("CAFE_data")
armStats(CAFE_data,chromNum="ALL",samples=c(1,3),arm="p")