Nothing
## ---- echo = FALSE, message = FALSE--------------------------------------
knitr::opts_chunk$set(collapse = T, comment = "#>")
options(tibble.print_min = 4L, tibble.print_max = 4L)
library(rSEA)
## ----data_sim------------------------------------------------------------
set.seed(753) #to get the same result as you repeat
names<-sapply(1:300, function(i) paste0( combn(letters, 2)[,i], collapse = "")) # a vector of two-letter names
p<-c(runif(100, 0, 1)^6,runif(200, 0, 1)) # a vector of random p-values, the first 100 are smaller
simdat<-data.frame(pvals=p, ids=names, stringsAsFactors=FALSE) #the dataframe
head(simdat) #take a look at the dataset
pathsize<-floor(runif(50, 10, 60)) #generate a vector of random pathway sizes between 10 and 60
mocklist<-lapply(pathsize,function(x) sample(names,size=x)) # create a pseudo list of pathways
## ----setTDP_chunk1-------------------------------------------------------
require(rSEA) #load rSEA
#setTDP(pvals, ids, data=simdat)
setTDP(simdat$pvals, simdat$ids)
## ----setTDP_chunk2-------------------------------------------------------
require(rSEA) #load rSEA
setTDP(simdat$pvals, simdat$ids, set=mocklist[[3]])
## ----setTest_chunk1------------------------------------------------------
require(rSEA)
#selfcontained test of all features
setTest(pvals, ids, data=simdat, testype = "selfcontained")
#default comp. test
setTest(pvals, ids, data=simdat, set=mocklist[[3]], testype = "competitive")
#custom comp. test
setTest(pvals, ids, data=simdat, set=mocklist[[3]], testype = "competitive", testvalue = 0.5)
## ----SEA_chunk1----------------------------------------------------------
require(rSEA) #load rSEA
testchart1<-SEA(simdat$pvals, simdat$ids, pathlist = mocklist)
head(testchart1)
## ----SEA_chunk2----------------------------------------------------------
require(rSEA) #load rSEA
testchart2<-SEA(pvals, ids, data=simdat, pathlist = mocklist, select =11:30)
testchart2
## ----setTest_chunk2------------------------------------------------------
require(rSEA) #load rSEA
lap<-union(mocklist[[8]], mocklist[[9]]) # the overlapping feature-set
length(lap)
setTDP(pvals, ids, data=simdat, set =lap)
setTest(pvals, ids, data=simdat, set =lap , testype = "selfcontained")
setTest(pvals, ids, data=simdat, set =lap , testype = "competitive", testvalue = 0.1)
## ----SEA_chunk3----------------------------------------------------------
require(rSEA) #load rSEA
testchart3<-topSEA(testchart1) #sorted by large TDP.estimates
head(testchart3)
testchart4<-topSEA(testchart1, by=Comp.adjP, descending=FALSE) #sorted by smallest competitive adj.p-values
head(testchart3)
sigchart<-topSEA(testchart1, by=Comp.adjP, thresh = 0.05) #keep only significant self-contained p-values
sigchart2<-topSEA(sigchart, by=Size, descending=TRUE) #sorted by pathway size
head(sigchart2)
## ----pathlist_chunk1, eval = FALSE---------------------------------------
#
# if (!requireNamespace("BiocManager", quietly = TRUE))
# install.packages("BiocManager")
#
# BiocManager::install("hgu133a.db")
#
# ###if you are running an older version of R
# #source("http://bioconductor.org/biocLite.R")
# #biocLite(c("limma","edgeR"))
## ----pathlist_chunk2, eval = FALSE---------------------------------------
# library(hgu133a.db)
# ls("package:hgu133a.db")
# columns(hgu133a.db)
#
# gobimap<-toTable(hgu133aGO)
# gobimap<-gobimap[gobimap$Ontology=="CC",]
#
# head(gobimap)
#
## ----pathlist_chunk3, eval = FALSE---------------------------------------
#
# GOIDs<-unique(gobimap$go_id)
# GOList<-lapply(GOIDs,
# function(id)
# gobimap$probe_id[gobimap$go_id==id])
#
# names(GOList)<-GOIDs
# #head(GOList)
#
# #make sure the Ids are unique and the paths are non-empty
# GOList<-lapply(GOList, unique)
# GOList <- lapply(GOList, function(path) if (all(is.na(path))) character(0) else path)
#
# #save(GOList, file="GOList.RData")
## ----pathlist_chunk4, eval = FALSE---------------------------------------
# if (!requireNamespace("BiocManager", quietly = TRUE))
# install.packages("BiocManager")
#
# BiocManager::install("org.Mm.eg.db")
#
# library(org.Mm.eg.db)
# ls("package:org.Mm.eg.db")
# columns(org.Hs.eg.db)
#
## ----pathlist_chunk5, eval = FALSE---------------------------------------
#
#
# uniKeys <- keys(org.Hs.eg.db, keytype="ENTREZID")
# cols <- c("SYMBOL", "PATH")
#
# keggbimap<-select(org.Hs.eg.db, keys=uniKeys,
# columns=cols, keytype="ENTREZID")
#
# head(keggbimap)
#
# keggIDs<-unique(keggbimap$PATH)
# KEGGList<-lapply(keggIDs,
# function(id)
# keggbimap$ENTREZID[keggbimap$PATH==id])
# names(KEGGList)<-keggIDs
# head(KEGGList)
#
# #make sure the Ids are unique and the paths are non-empty
# KEGGList<-lapply(KEGGList, unique)
# KEGGList<-lapply(KEGGList, function(path)
# path[!is.na(path)])
# KEGGList <- lapply(KEGGList,
# function(path)
# if (all(is.na(path))) character(0) else path)
#
# #save(KEGGList, file="KEGGList.RData")
#
## ----pathlist_chunk6, eval = FALSE---------------------------------------
#
# if (!requireNamespace("BiocManager", quietly = TRUE))
# install.packages("BiocManager")
#
# BiocManager::install("rWikiPathways")
#
## ----pathlist_chunk7, eval = FALSE---------------------------------------
#
# #Matching the IDs to create list of wikipathways for metabs
# library(rWikiPathways)
#
# homoPathways<-listPathwayIds(organism="Homo sapiens")
# wikiList<-lapply(homoPathways,
# function(x)
# getXrefList(pathway = x, systemCode="En"))
#
# names(wikiList)<-homoPathways
#
# #make sure the Ids are unique and the paths are non-empty
# wikiList<-lapply(wikiList, unique)
# wikiList <- lapply(wikiList, function(path) if (all(is.na(path))) character(0) else path)
#
# #save(wikiList, file="wikiList.RData")
#
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