Description Usage Arguments Value Author(s)
Function to calculate a overrepresentation analysis based on gene ontology using a one-sided hypergeometric test for given genes.
1 2 3 | ORA(NCBIs, Correction = "BON", PvalueThreshold = 0.05, MinNrOfGenes = 2,
OnlyManuCur = FALSE, RefSet = NULL, GOAall = ReadLRN("GOAall.lrn",
system.file("extdata",package = "ORA")))
|
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". |
ORAresults |
List of 4:
|
CL
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.