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

Description Usage Arguments Author(s) See Also

Description

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

Usage

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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' or 'png'.

Author(s)

CL

See Also

dbtORA.


CLippmann/dbtORA documentation built on May 26, 2019, 6:40 a.m.