armStats: Find aberrations with chromosome arm resolution

In CAFE: Chromosmal Aberrations Finder in Expression data

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.

Note

Technically speaking, the Fisher's exact test is better than the chi-square test; the Fisher's exact test gives an exact p-value, whereas the chi-square test only gives an approximation. However, the Fisher's exact test can get slow for large sample sizes, and the chi-square test becomes better with increasing sample size but does not slow down as much.

Author(s)

Sander Bollen

See Also

chromosomeStats bandStats

Examples

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

CAFE documentation built on Nov. 8, 2020, 7:44 p.m.