SAFE-class: Class SAFE

In safe: Significance Analysis of Function and Expression

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.

Author(s)

William T Barry: [e-mail]

See Also

safe, safeplot.

safe documentation built on Nov. 8, 2020, 5:37 p.m.