vignettes/goSorensen_Introduction.R

In pablof1988/goSorensen: Statistical inference based on the Sorensen-Dice dissimilarity and the Gene Ontology (GO)

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## ----setup, include=FALSE-----------------------------------------------------
knitr::opts_chunk$set(
  comment = ""
)

## ----env, message = FALSE, warning = FALSE, echo = TRUE-----------------------
library(goSorensen)

## ----eval=FALSE---------------------------------------------------------------
# if (!requireNamespace("goSorensen", quietly = TRUE)) {
#     BiocManager::install("goSorensen")
# }
# library(goSorensen)

## -----------------------------------------------------------------------------
data("allOncoGeneLists")

## -----------------------------------------------------------------------------
sapply(allOncoGeneLists, length)

# First 15 gene identifiers of gene lists atlas and sanger:
allOncoGeneLists[["atlas"]][1:15]
allOncoGeneLists[["sanger"]][1:15]

## ----message = FALSE, warning = FALSE, eval = FALSE---------------------------
# if (!requireNamespace("org.Hs.eg.db", quietly = TRUE)) {
#     BiocManager::install("org.Hs.eg.db")
# }

## ----message = FALSE, warning = FALSE, eval = TRUE----------------------------
library(org.Hs.eg.db)

## ----message = FALSE, warning = FALSE, echo = TRUE----------------------------
humanEntrezIDs <- keys(org.Hs.eg.db, keytype = "ENTREZID")

## ----echo=FALSE---------------------------------------------------------------
options(max.print = 50)

## ----eval=TRUE----------------------------------------------------------------
enrichedAtlas <- enrichedIn(allOncoGeneLists[["atlas"]],
           geneUniverse = humanEntrezIDs, 
           orgPackg = "org.Hs.eg.db",
           onto = "BP", GOLevel = 4)
enrichedAtlas

## -----------------------------------------------------------------------------
fullEnrichedAtlas <- enrichedIn(allOncoGeneLists[["atlas"]],
           geneUniverse = humanEntrezIDs, 
           orgPackg = "org.Hs.eg.db",
           onto = "BP", GOLevel = 4, 
           onlyEnriched = FALSE)
fullEnrichedAtlas

## -----------------------------------------------------------------------------
# number of GO terms in enrichedAtlas
length(enrichedAtlas)

# number of GO terms in fullEnrichedAtlas
length(fullEnrichedAtlas)

## ----echo=FALSE---------------------------------------------------------------
options(max.print = 100)

## ----eval=FALSE---------------------------------------------------------------
# enrichedInBP4 <- enrichedIn(allOncoGeneLists,
#                                geneUniverse = humanEntrezIDs,
#                                orgPackg = "org.Hs.eg.db",
#                                onto = "BP", GOLevel = 4)
# enrichedInBP4

## ----echo=FALSE---------------------------------------------------------------
data("enrichedInBP4")
enrichedInBP4

## ----eval=FALSE---------------------------------------------------------------
# fullEnrichedInBP4 <- enrichedIn(allOncoGeneLists,
#                                geneUniverse = humanEntrezIDs,
#                                orgPackg = "org.Hs.eg.db",
#                                onto = "BP", GOLevel = 4,
#                                onlyEnriched = FALSE)
# fullEnrichedInBP4

## ----echo=FALSE---------------------------------------------------------------
data("fullEnrichedInBP4")
fullEnrichedInBP4

## -----------------------------------------------------------------------------
# number of GO terms (rows) in enrichedInBP4
nrow(enrichedInBP4)

# number of GO terms (rows) in fullEnrichedInBP4
nrow(fullEnrichedInBP4)

## ----eval=FALSE---------------------------------------------------------------
# cont_atlas.sanger_BP4 <- buildEnrichTable(allOncoGeneLists$atlas,
#                                           allOncoGeneLists$sanger,
#                                           listNames = c("atlas", "sanger"),
#                                           geneUniverse = humanEntrezIDs,
#                                           orgPackg = "org.Hs.eg.db",
#                                           onto = "BP",
#                                           GOLevel = 4)
# cont_atlas.sanger_BP4

## ----echo=FALSE---------------------------------------------------------------
data("cont_atlas.sanger_BP4")
cont_atlas.sanger_BP4

## ----eval=FALSE---------------------------------------------------------------
# cont_all_BP4 <- buildEnrichTable(allOncoGeneLists,
#                                  geneUniverse = humanEntrezIDs,
#                                  orgPackg = "org.Hs.eg.db",
#                                  onto = "BP",
#                                  GOLevel = 4)

## ----eval=FALSE---------------------------------------------------------------
# allContTabs <- allBuildEnrichTable(allOncoGeneLists,
#                                    geneUniverse = humanEntrezIDs,
#                                    orgPackg = "org.Hs.eg.db",
#                                    ontos = c("BP", "CC", "MF"),
#                                    GOLevels = 3:10)

## ----eval=FALSE---------------------------------------------------------------
# eqTest_atlas.sanger_BP4 <- equivTestSorensen(allOncoGeneLists$atlas,
#                                              allOncoGeneLists$sanger,
#                                              listNames = c("atlas", "sanger"),
#                                              geneUniverse = humanEntrezIDs,
#                                              orgPackg = "org.Hs.eg.db",
#                                              onto = "BP", GOLevel = 4,
#                                              d0 = 0.4444,
#                                              conf.level = 0.95)
# eqTest_atlas.sanger_BP4

## ----echo=FALSE---------------------------------------------------------------
data("eqTest_atlas.sanger_BP4")
eqTest_atlas.sanger_BP4

## -----------------------------------------------------------------------------
equivTestSorensen(cont_atlas.sanger_BP4, 
                  d0 = 0.4444, 
                  conf.level = 0.95)

## -----------------------------------------------------------------------------
upgrade(eqTest_atlas.sanger_BP4, d0 = 0.2857, 
        conf.level = 0.99, boot = TRUE)

## ----eval=FALSE---------------------------------------------------------------
# eqTest_all_BP4 <- equivTestSorensen(allOncoGeneLists,
#                                     geneUniverse = humanEntrezIDs,
#                                     orgPackg = "org.Hs.eg.db",
#                                     onto = "BP",
#                                     GOLevel = 4,
#                                     d0 = 0.4444,
#                                     conf.level = 0.95)

## ----eval=FALSE---------------------------------------------------------------
# eqTest_all_BP4 <- equivTestSorensen(cont_all_BP4,
#                                     d0 = 0.4444,
#                                     conf.level = 0.95)

## ----echo=FALSE---------------------------------------------------------------
data(eqTest_all_BP4)

## ----echo=FALSE---------------------------------------------------------------
options(digits = 4)

## -----------------------------------------------------------------------------
getDissimilarity(eqTest_all_BP4, simplify = FALSE)

## -----------------------------------------------------------------------------
getPvalue(eqTest_all_BP4, simplify = FALSE)

## ----eval=FALSE---------------------------------------------------------------
# allEqTests <- allEquivTestSorensen(allOncoGeneLists,
#                                    geneUniverse = humanEntrezIDs,
#                                    orgPackg = "org.Hs.eg.db",
#                                    ontos = c("BP", "CC", "MF"),
#                                    GOLevels = 3:10,
#                                    d0 = 0.4444,
#                                    conf.level = 0.95)

## ----eval=FALSE---------------------------------------------------------------
# allEqTests <- allEquivTestSorensen(allContTabs,
#                                    d0 = 0.4444,
#                                    conf.level = 0.95)

## ----sessionInfo--------------------------------------------------------------
sessionInfo()