SAFE-class: Class SAFE

In lgeistlinger/safe: Significance Analysis of Function and Expression

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" 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.

lgeistlinger/safe documentation built on Aug. 4, 2023, 7:34 p.m.