ORAfilename: Function to complete the OutFile name passed to dbtORA with...

In CLippmann/dbtORA: Overrepresentation Analysis

Description

Function to complete the OutFile name passed to dbtORA with ORA parameters.

Usage

ORAfilename(OutFile, NrOfValidInputGenes, Correction, PvalueThreshold, MinNrOfGenes, 
OnlyManuCur, WithRefSet = FALSE)

Arguments

OutFile	String; Filename of the output file(s). Will be complemented by the parameters of the ORA.
NrOfValidInputGenes	String; Number of valid input genes = #(input genes) - #(duplicated and non-annotated genes)
Correction	String; Type of correction for mulitple testing of the p-values. 'BON' for Bonferroni, 'FDR' for False Discovery Rate, 'RAW' if no correction should be done.
PvalueThreshold	Numeric; P-value threshold. GO-Terms with p-values greater than PvalueThreshold will be ignored.
MinNrOfGenes	Numeric; Minimum number of genes annotated to one Term that is accepted. Only GO terms with more than MinNrOfGenes genes will be considered in calculation.
OnlyManuCur	Boolean; Set TRUE if only manually curated gene annotations should be considered.
WithRefSet	Boolean; Default: FALSE. Set TRUE if a reference set of genes is used.

Value

OutFilePlusParams

String; The complemented OutFile.

Author(s)

CL

See Also

dbtORA

CLippmann/dbtORA documentation built on Feb. 4, 2020, 12:37 a.m.