SAFE-class {safe}R Documentation

Class SAFE

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" describing 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" describing the local 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" describing the method used to estimate error rates across multiple comparisons.
global.error:
Object of class "numeric" containing the (unsorted) error rates associated with the p-values for categories. If not computed, it will be set to NA.
C.mat:
Object of class "matrix" containing the category assignments. Each row corresponds to a gene, and each column a category.
alpha:
Object of class "numeric" containing the alpha level for significance of a category.
method:
Object of class "character" describing the resampling method used in safe.

Methods

show
(SAFE): Summarizes the test results of significant categories.
"["
(SAFE): Extracts results of one or more category.
safeplot
(SAFE): The safeplot produces a plot of the relative association of expression in a category of genes relative to their complement.

Author(s)

William T Barry: wbarry@bios.unc.edu

See Also

safe, safeplot.


[Package safe version 1.0.0 Index]