ORA: Function to calculate a overrepresentation analysis.

In CLippmann/ORA: Overrepresentation Analysis

Description

Function to calculate a overrepresentation analysis based on gene ontology using a one-sided hypergeometric test for given genes.

Usage

ORA(NCBIs, Correction = "BON", PvalueThreshold = 0.05, MinNrOfGenes = 2, 
OnlyManuCur = FALSE, RefSet = NULL, GOAall = ReadLRN("GOAall.lrn", 
system.file("extdata",package = "ORA")))

Arguments

NCBIs	Numeric; Vector of NCBI numbers of genes in sample (gene set of interest).
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.
PvalueThreshold	Numeric; Default: 0.05 P-value threshold. GO terms with p-values greater than PvalueThreshold will be ignored.
MinNrOfGenes	Numeric; Default: 2 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; Default: TRUE Set TRUE if only manually curated gene annotations should be considered.
RefSet	Numeric; Default: NULL Vector of NCBI numbers of genes that form the reference set (universe). If not given i.e. NULL or missing, all known genes are taken as universe.
GOAall	Lrn-File containing all direct and indirect annotations of genes to GOterms as sparse Matrix. File can be found in system.file("extdata", package = 'ORA'), called "GOAall.lrn".

Value

ORAresults

List of 4: LRNresults List of 16: Information needed to generate the lrn file containing all the calculated values for the GO terms found to be significant for input genes. LRNresults$GOtermNr Numeric; GO term numbers found to be significant for input genes. LRNresults$OntologyNr Numeric; Number of ontology (1=BP, 2=MF, 4=CC). LRNresults$NrOfGenesInUniverse Numeric; Number of genes in universe used for p-value computation. LRNresults$NrOfGenesInSample Numeric; Number of input genes used for p-value computation. LRNresults$NrOfAnnotationsInTerm Numeric; Number of annotations associated to GO term. LRNresults$Up Numeric; 1 if GO term is up regulated (expected < observed), 0 if down. LRNresults$ExpNrOfAnnsInTerm Numeric; Statistically expected number of genes annotated to GO term. LRNresults$ObservedNrOfAnnsInTerm Numeric; Empirically observed number of genes annotated to GO term. LRNresults$RelDiff Numeric; Relative difference of expected and observed in percent. LRNresults$Pvalue Numeric; Pvalues for each GO term received by statistical test. LRNresults$LogPvalue Numeric; log(Pvalues). LRNresults$Certainty Numeric; Certainty value. See certainty. LRNresults$InfoValue Numeric; Value describing partial Shannon information. See infoValue. LRNresults$Remarkable Numeric; Product of Certainty and InfoValue. LRNresults$Importance Numeric; Minimum of Certainty and InfoValue. LRNresults$InfoContent Numeric; InformationContent from GOTermInfosBP/MF/CC.lrn depending on OnlyManuCur. LRNresults$InfoContentORA Numeric; -log2(ObservedNrOfAnnsInTerm/NrOfGenesInSample) LRNresults$IsHeadline Boolean; 1 if GO term is headline, 0 if not. LRNresults$IsDetail Boolean; 1 if GO term is detail, 0 if not. NAMESresults List of 3: Information needed to generate the names file containing information about GO terms. NAMESresults$GOtermNr Numeric; GO term numbers found to be significant for input genes. NAMESresults$GOtermDescription String; Description of GO terms = termDescription(GOtermId). NAMESresults$GOtermId String; GO term Id = termId(GOtermNr). Genes2GOtermsMatrix Numeric; matrix explaining the connection of genes and GO terms. Genes2GOtermsMatrix[i,j]==1 iff gene in ith row is annotated to GO term in jth row. GO2GOAdjMatrices List of 4: Adjacency matrices for each ontology and combined sparse matrix. GO2GOAdjMatrices$GO2GOAdjMatrix Numeric; Block diagonal adjacency matrix (formal class dgCMatrix from package Matrix) describing the complete directed acyclic graph (DAG) of the significant GOterms up to the root, i.e. the edges between GOterms and their parents. GO2GOAdjMatrix[i,j]== 1 iff i is parent of j. First row contains numbers 1, 2, and 4 specifying the ontology BP, MF, and CC. GO2GOAdjMatrices$AdjMatrixGO2GOBP Numeric; (non-sparse) Adjacency matrix of BP-DAG. AdjMatrixGO2GOBP[i,j]==1 iff i is parent of j. GO2GOAdjMatrices$AdjMatrixGO2GOMF Numeric; (non-sparse) Adjacency matrix of MF-DAG. AdjMatrixGO2GOBP[i,j]==1 iff i is parent of j. GO2GOAdjMatrices$AdjMatrixGO2GOCC Numeric; (non-sparse) Adjacency matrix of CC-DAG. AdjMatrixGO2GOBP[i,j]==1 iff i is parent of j.

Author(s)

CL

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