gexmap {GExMap} | R Documentation |
GExMap analyze genomic distribution and GO of genes lists produced by transcriptomic studies.
gexmap(genome = "homosapiens", scale = "", source = "", res = "", isGO = TRUE, isMAP = TRUE, lim_chi = 5, global_test_choice = 4, pcorrd = 2, pcorrv = 1)
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). |
Nicolas Cagnard <nicolas.cagnard@inserm.fr>
http://gexmap.site.voila.fr/
gexmap(genome="homosapiens", scale="", source="test", res="", isGO=TRUE, isMAP=TRUE, lim_chi=5, global_test_choice=4, pcorrd=2, pcorrv=1)