twoGroupsGO: Performs the GO analysis for two groups

In uzh/ezRun: An R meta-package for the analysis of Next Generation Sequencing Data

Performs the GO analysis for two groups

Description

Performs the GO analysis for two groups.

Usage

twoGroupsGO(
  param,
  testResult,
  seqAnno,
  normalizedAvgSignal = NULL,
  method = "Wallenius"
)

ezGoseq(
  param,
  selectedGenes,
  allGenes,
  gene2goList = NULL,
  method = c("Wallenius", "Sampling", "Hypergeometric"),
  onto = NULL,
  normalizedAvgSignal = NULL
)

Arguments

param	a list of parameters: featureLevel which feature level to use. pValThreshGO a numeric specifying the threshold for the GO p-value. log2RatioThreshGO a numeric specifying the threshold for the GO log2 ratios. includeGoParentAnnotation a logical indicating whether to include the annotation of the GO parents.
testResult	a list containing the results of an earlier test.
seqAnno	the sequence annotation.
normalizedAvgSignal	an optional normalized average signal.
method	which method to pass to ezGoseq().

Value

Returns the results of the GO analysis.

Functions

• ezGoseq: Performs the GO analysis and returns a list of results.

Author(s)

Rehrauer, Hubert

Schmid, Peter

See Also

ezGoseq

uzh/ezRun documentation built on Dec. 26, 2024, 9:53 a.m.