Description Usage Arguments Author(s) See Also
View source: R/checkORAparameters.R
Function to check if the parameters passed to dbtORA
are correct.
1 2 3 4 5 | checkORAparameters(InFileWithExt, InFileDirectory, RefSetFileWithExt,
RefSetDirectory, OutFile, OutFileDirectory, Correction, PvalueThreshold,
MinNrOfGenes, OnlyManuCur, drawDAG, MarkDetails, MarkHeadlines, PlotExt)
|
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'. |
CL
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