Description Usage Arguments Value Note Author(s) See Also Examples
View source: R/chromosomeStats.R
Calculate significant chromosomal arms with various statistical tests
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datalist 
The CAFE datalist to be analyzed, i.e. the output of

chromNum 
The chromosome to be calculated. This can be 
arm 
Select which arm  
samples 
A vector containing sample numbers to be analyzed 
select 
Signifies which type of sample selection prompt will be shown, if

test 
Signifies which statistical test to be used in the final calculation. Must be
either 
bonferroni 
If 
enrichment 
Test for over or underexpression. Can be set to 
A named vector containing pvalues.
Technically speaking, the Fisher's exact test is better than the chisquare test; the Fisher's exact test gives an exact pvalue, whereas the chisquare test only gives an approximation. However, the Fisher's exact test can get slow for large sample sizes, and the chisquare test becomes better with increasing sample size but does not slow down as much.
Sander Bollen
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