runDEAnalysis {ImpulseDE2}R Documentation

Perform differential expression analysis and identification of transiently activated or deactivated genes.

Description

Performs model selction based on loglikelihood ratio tests. The primary model selection is the differential expression analysis. The secondary model selection is the selection between a sigmoidal and an impulse fit for differentially expressed genes which is used to define transiently activated or deactivated genes.

Usage

runDEAnalysis(objectImpulseDE2, boolCaseCtrl, boolIdentifyTransients,
  scaQThresTransients = 0.001)

Arguments

objectImpulseDE2

(object class ImpulseDE2Object) Object containing fits to be evaluated.

boolCaseCtrl

(bool) Whether to perform case-control analysis. Does case-only analysis if FALSE.

boolIdentifyTransients

(bool) [Defaul FALSE] Whether to identify transiently activated or deactivated genes. This involves an additional fitting of sigmoidal models and hypothesis testing between constant, sigmoidal and impulse model.

scaQThresTransients

(scalar) [Default 0.001] FDR-corrected p-value threshold for hypothesis tests between impulse, sigmoidal and constant model used to identify transiently regulated genes.

Value

(ImpulseDE2Object) Input object with dfDEAnalysis updated to: dfDEAnalysis (data frame samples x reported characteristics) Summary of fitting procedure and differential expression results for each gene.

Entries only present in case-only DE analysis:

Entries only present in case-control DE analysis:

Entries only present if boolIdentifyTransients is TRUE:

Author(s)

David Sebastian Fischer

See Also

Called by runImpulseDE2.


[Package ImpulseDE2 version 1.4.0 Index]