## ----style, echo = FALSE, results = 'asis'------------------------------------ BiocStyle::markdown() ## ----setup, include=FALSE----------------------------------------------------- knitr::opts_chunk$set(dpi=25,fig.width=7) ## ----env, message = FALSE, warning = FALSE, echo = TRUE----------------------- library(goSorensen) ## ----eval=FALSE--------------------------------------------------------------- # ## Only if BiocManager is not previosly installed: # install.packages("BiocManager") # # ## otherwise, directly: # BiocManager::install("goSorensen") ## ----eval=FALSE--------------------------------------------------------------- # devtools::install_github("pablof1988/goSorensen", build_vignettes = TRUE) ## ----------------------------------------------------------------------------- data("allOncoGeneLists") ## ----------------------------------------------------------------------------- data("humanEntrezIDs") length(allOncoGeneLists) sapply(allOncoGeneLists, length) # First 20 gene identifiers of gene lists Vogelstein and sanger: allOncoGeneLists[["Vogelstein"]][1:20] allOncoGeneLists[["sanger"]][1:20] # Build the enrichment contingency table between gene lists Vogelstein and # sanger for the MF ontology at GO level 5: enrichTab <- buildEnrichTable(allOncoGeneLists[["Vogelstein"]], allOncoGeneLists[["sanger"]], geneUniverse = humanEntrezIDs, orgPackg = "org.Hs.eg.db", onto = "MF", GOLevel = 5, listNames = c("Vogelstein", "sanger")) enrichTab # Equivalence test for an equivalence (or negligibility) limit 0.2857 testResult <- equivTestSorensen(enrichTab, d0 = 0.2857) testResult ## ----------------------------------------------------------------------------- equivTestSorensen(allOncoGeneLists[["Vogelstein"]], allOncoGeneLists[["sanger"]], d0 = 0.2857, geneUniverse = humanEntrezIDs, orgPackg = "org.Hs.eg.db", onto = "MF", GOLevel = 5, listNames = c("Vogelstein", "sanger")) ## ----------------------------------------------------------------------------- boot.testResult <- equivTestSorensen(enrichTab, d0 = 0.2857, boot = TRUE) boot.testResult ## ----------------------------------------------------------------------------- getDissimilarity(testResult) getSE(testResult) getPvalue(testResult) getTable(testResult) getUpper(testResult) # In the bootstrap approach, only these differ: getPvalue(boot.testResult) getUpper(boot.testResult) # (Only available for bootstrap tests) efective number of bootstrap resamples: getNboot(boot.testResult) ## ----------------------------------------------------------------------------- # The dissimilarity: dSorensen(enrichTab) # Or from scratch, directly from both gene lists: dSorensen(allOncoGeneLists[["Vogelstein"]], allOncoGeneLists[["sanger"]], geneUniverse = humanEntrezIDs, orgPackg = "org.Hs.eg.db", onto = "MF", GOLevel = 5, listNames = c("Vogelstein", "sanger")) # The first option is faster, it avoids internally building the enrichment # contingency table # Its standard error: seSorensen(enrichTab) # or: seSorensen(allOncoGeneLists[["Vogelstein"]], allOncoGeneLists[["sanger"]], geneUniverse = humanEntrezIDs, orgPackg = "org.Hs.eg.db", onto = "MF", GOLevel = 5, listNames = c("Vogelstein", "sanger")) # Upper limit of the confidence interval for the true distance: duppSorensen(enrichTab) duppSorensen(enrichTab, conf.level = 0.90) duppSorensen(enrichTab, conf.level = 0.90, boot = TRUE) duppSorensen(allOncoGeneLists[["Vogelstein"]], allOncoGeneLists[["sanger"]], geneUniverse = humanEntrezIDs, orgPackg = "org.Hs.eg.db", onto = "MF", GOLevel = 5, listNames = c("Vogelstein", "sanger")) ## ----------------------------------------------------------------------------- dSorensen(allOncoGeneLists, onto = "MF", GOLevel = 5, geneUniverse = humanEntrezIDs, orgPackg = "org.Hs.eg.db") ## ----------------------------------------------------------------------------- allTests <- equivTestSorensen(allOncoGeneLists, d0 = 0.2857, onto = "MF", GOLevel = 5, geneUniverse = humanEntrezIDs, orgPackg = "org.Hs.eg.db") getPvalue(allTests) getDissimilarity(allTests, simplify = FALSE) ## ----------------------------------------------------------------------------- enrichMat <- matrix(c(20, 1, 9, 2149), nrow = 2) enrichMat dSorensen(enrichMat) enrichVec <- c(20, 1, 9, 2149) equivTestSorensen(enrichVec) equivTestSorensen(enrichVec, boot = TRUE) len3Vec <- c(20, 1, 9) dSorensen(len3Vec) seSorensen(len3Vec) duppSorensen(len3Vec) # Error, bootstrapping requires the full (4 values) contingency table: try(duppSorensen(len3Vec, boot = TRUE), TRUE) ## ----sessionInfo-------------------------------------------------------------- sessionInfo()