gextest {GExMap} | R Documentation |
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 .
gextest(genome.test, nhazard, results.graph, lim_chi, global_test_choice, pcorrd, pcorrv)
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" |
This function is included in the GExMap package and could not be used independently.
Nicolas Cagnard <nicolas.cagnard@inserm.fr>
GExMap