gexmap: Main function of the GExMap package

Description Usage Arguments Author(s) References

View source: R/gexmap.R

Description

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

Usage

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

Arguments

genome

Annotation data and genomic localizations for all genes of a specific genome

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@gmail.com>

References

http://gexmap.voila.net/index.html Research Article JPB/Vol.2.1 051- 059(2009)/January 2009 doi:10.4172/jpb.1000060 GExMap: An Intuitive Visual Tool to Detect and Analyze Genomic Distribution in Microarray-generated Lists of Differentially Expressed Genes Nicolas Cagnard, Carlo Lucchesi, Gilles Chiocchia


GExMap documentation built on May 30, 2017, 1:46 a.m.