checkORAparameters: Function to check if the parameters passed to 'dbtORA' are...

In CLippmann/ORA: Overrepresentation Analysis

Description

Function to check if the parameters passed to dbtORA are correct.

Usage

checkORAparameters(InFileWithExt, InFileDirectory, RefSetFileWithExt, 

RefSetDirectory, OutFile, OutFileDirectory, Correction, PvalueThreshold,

MinNrOfGenes, OnlyManuCur, drawDAG, MarkDetails, MarkHeadlines, PlotExt)

Arguments

InFileWithExt	String; Filename with extension where NCBIs are keys (for *.names and *.lrn files) or the only column (for *.txt files).
InFileDirectory	String; Directory where InFileWithExt can be found.
RefSetFileWithExt	String; Filename with extension where NCBIs are keys (for *.names and *.lrn files) or the only column (for *.txt files). NCBIs will be used as reference set.
RefSetDirectory	String; Directory where RefSetFileWithExt with reference NCBIs can be found.
OutFile	String; Filename of the output file(s). Will be complemented by the parameters of the ORA.
OutFileDirectory	String; Directory where results of ORA and DAGs will be saved.
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. GO-Terms with more than MinNrOfGenes annotated genes will be considered in calculation.
OnlyManuCur	Boolean; Set TRUE if only manually curated gene annotations should be considered.
drawDAG	Boolean; Set TRUE if directed acyclic graphs (DAGs) should be drawn. If drawDAG is set to FALSE, the parameters MarkDetails, MarkHeadlines and CurtDAG will be ignored.
MarkDetails	Boolean; Set TRUE if details of the DAG should be marked in blue colour.
MarkHeadlines	Boolean; Set TRUE if headlines of the DAG should be marked in yellow colour.
PlotExt	String; Extension of the plotfile showing the DAG. One of 'pdf' , 'eps', 'svg' or 'png'.

Author(s)

CL

See Also

dbtORA.

CLippmann/ORA documentation built on Feb. 4, 2020, 9:38 p.m.