gextest {GExMap}R Documentation

Perform the statistical analysis step

Description

This function selects the chromosoms by two global tests comparing an estimated hazard genomic distribution to the real distribution extracted from the user list. If the chromosom is selected, a local analysis is performed to localize and test regions of interest .

Usage

gextest(genome.test, nhazard, results.graph, lim_chi, global_test_choice, pcorrd, pcorrv)

Arguments

genome.test All genomic data to be tested.
nhazard Total number of genes of the hazard distribution.
results.graph Data necessary to produces the graphic files.
lim_chi Limit of genes to perform the CHI squared global test (set to 5 by default).
global_test_choice Choice of chromosomes selection according to the results of the global statistical tests (see gextest() function).\ 1- At least CHI is OK\ 2- At least Wilcoxon is OK\ 3- CHI & Wilcoxon are OK\ 4- CHI OR Wilcoxon is OK\ Default value is set at 4.
pcorrd Choice of pvalue correction method for the global tests:\ 1- "Bonferroni" 2- "Holm" 3- "Hochberg" 4- "SidakSS" 5- "SidakSD" 6- "BH" 7- "BY"
pcorrv Choice of pvalue correction method for the local tests:\ 1- "Bonferroni" 2- "Holm" 3- "Hochberg" 4- "SidakSS" 5- "SidakSD" 6- "BH" 7- "BY"

Details

This function is included in the GExMap package and could not be used independently.

Author(s)

Nicolas Cagnard <nicolas.cagnard@inserm.fr>

See Also

GExMap


[Package GExMap version 1.0 Index]