Usage
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).