dbtORA: Function to do an ORA including the drawing of DAGs.

In CLippmann/ORA: Overrepresentation Analysis

Description

Function to do an Overrepresentation Analysis (ORA) including the drawing of the directed acyclic graphs (DAGs) of the resulting GO terms.

Usage

dbtORA(InFileWithExt, PvalueThreshold = 0.05, Correction = "BON", OnlyManuCur = TRUE, 

MinNrOfGenes = 2, InFileDirectory = getwd(), OutFile = InFileWithExt, 

OutFileDirectory = InFileDirectory, RefSetFileWithExt = NULL, 

RefSetDirectory = InFileDirectory, drawDAG = TRUE, MarkDetails = TRUE, 

MarkHeadlines = TRUE, PlotExt = "png")

Arguments

InFileWithExt	String; Filename with extension where NCBIs are keys (for *.names and *.lrn files) or the only column (for *.txt files).
PvalueThreshold	Numeric; Default: 0.05 P-value threshold. GO terms with p-values greater than PvalueThreshold will be ignored.
Correction	String; Default: 'BON' 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.
OnlyManuCur	Boolean; Default: TRUE Set TRUE if only manually curated gene annotations should be considered.
MinNrOfGenes	Numeric; Default: 2 Minimum number of genes annotated to one Term that is accepted. Only GO terms with more than MinNrOfGenes annotated genes will be considered in calculation.
InFileDirectory	String; Default: current directory getwd(). Directory where InFileWithExt can be found.
OutFile	String; Default: InFileWithExt (extension will be adjusted) Filename of the output file(s). Will be complemented by the parameters of the ORA.
OutFileDirectory	String; Default: InFileDirectory Directory where results of ORA and DAGs will be saved.
RefSetFileWithExt	String; Default: NULL 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; Default: InFileDirectory Directory where RefSetFileWithExt with reference NCBIs can be found.
drawDAG	Boolean; Default: TRUE Set TRUE if DAGs should be drawn. If drawDAG is set to FALSE, the parameters MarkDetails, MarkHeadlines and CurtDAG will be ignored.
MarkDetails	Boolean; Default: TRUE Set TRUE if details of the DAG should be marked in blue colour.
MarkHeadlines	Boolean; Default: TRUE Set TRUE if headlines of the DAG should be marked in yellow colour.
PlotExt	String; Default: 'png' Extension of the plotfile showing the DAG. One of 'pdf', 'eps', 'svg' or 'png'.

Details

Wrapper function to execute mainly ORA and drawORA. Coloring of the nodes and its meaning: Red - Significantly overrepresented nodes; Green - Significantly underrepresented nodes; White - Terms that are important for DAG structure but do not have a significant p-value. If MarkHeadlines = TRUE, the significant(!) nodes with highest remarkable value in each path from a detail to the root get a yellow filling. The margin indicates over- or underrepesentation by its red or green color. If MarkDetails = TRUE, the details of the DAG will be colored in blue. The margin again indicates over- or underrepesentation by its red or green color. If MarkHeadlines and MarkDetails are TRUE, there might be nodes that are both headlines and details. In this case the nodes have a maring acording to over- or underrepesentation in red or green and are filled in yellow like all headlines. Additionally the writing is blue to indicate that this node is a detail.

Value

Various files containing all the information received by ORA, Genes to GO terms matrix, adjacency matrix of the GO terms and plots of the corresponding DAGs.

Author(s)

CL

See Also

ORA, drawORA.

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