gexmap {GExMap}R Documentation

Main function of the GExMap package

Description

GExMap analyze genomic distribution and GO of genes lists produced by transcriptomic studies.

Usage

gexmap(genome = "homosapiens", scale = "", source = "", res = "", isGO = TRUE, isMAP = TRUE, lim_chi = 5, global_test_choice = 4, pcorrd = 2, pcorrv = 1)

Arguments

genome ~~Describe genome here~~
scale The variable scale is the scale used to produce the graphics and to perform the statistical tests. Customizable in input in the gexmap(scale="") main function, the scale is set to 1 000 000 bp by default.
source Folder which would contain alla data source as *.Rdata files.
res Folder which will contain the results data files and folders.
isGO TRUE/FALSE, customizable input variable to perform or no the Gene Ontology analysis of the tested gene list.
isMAP TRUE/FALSE, customizable input variable to perform or no the graphical reoprts of genomic analysis in pdf files.
lim_chi Limit number of gene necessary to perform the CHI squared global test to statistically select the chromosomes. (used in the gestest() function).
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 (see gextest() function).
pcorrv Choice of pvalue correction method for the local tests (see gextest() function).

Author(s)

Nicolas Cagnard <nicolas.cagnard@inserm.fr>

References

http://gexmap.site.voila.fr/

Examples

gexmap(genome="homosapiens", scale="", source="test", res="", isGO=TRUE, isMAP=TRUE, lim_chi=5, global_test_choice=4, pcorrd=2, pcorrv=1)

[Package GExMap version 1.0 Index]