Description
The class SAFE is the output from the function safe. It is also the input to the plotting function safeplot.
Slots
local:- Object of class
"character" indicating the local statistic used. local.stat:- Object of class
"numeric" containing the (unsorted) observed local statistics for genes. local.pval:- Object of class
"numeric" containing the (unsorted) empirical p-values for genes global:- Object of class
"character" indicating the global statistic used. global.stat:- Object of class
"numeric" containing the (unsorted) observed global statistics for categories. global.pval:- Object of class
"numeric" containing the (unsorted) empirical p-values for categories. error:- Object of class
"character" indicating the method used to estimate error rates across multiple comparisons. global.error:- Object of class
"numeric" containing the (unsorted) error rates (adjusted p-values) for categories. If not computed, it will be set to NA. C.mat:- Object of class
"SparseM" containing the category assignments. alpha:- Object of class
"numeric" containing the alpha level used in returning significant results. method:- Object of class
"character" indicating the resampling method used in safe.
Methods
- show
- (safe.results): Summarizes the test results of significant categories.
- [
- (safe.results): Returns a SAFE object for categories indicated by integer or character strings.
- safeplot
- (safe.results):
safeplot produces CDFs of the association of expression to phenotype in a category relative to its complement.