## ----echo=FALSE---------------------------------------------------------- knitr::opts_chunk$set(collapse = FALSE,comment = "#>",fig.pos='H') ## ----eval=TRUE, message=FALSE, warning=FALSE, results='hide'------------- # if (!requireNamespace("BiocManager", quietly=TRUE)) # install.packages("BiocManager") # BiocManager::install("PathwaySplice") library(PathwaySplice) ## ----eval = FALSE-------------------------------------------------------- # library(devtools) # install_github("SCCC-BBC/PathwaySplice") ## ----eval=TRUE, warning=FALSE, message=FALSE, results='markup'----------- data(featureBasedData) head(featureBasedData) ## ----eval=TRUE, message=FALSE, warning=FALSE, results='markup'----------- gene.based.table <- makeGeneTable(featureBasedData, stat = "pvalue") head(gene.based.table) ## ----eval=TRUE, warning=FALSE, message=FALSE, results='markup'----------- lrTestBias(gene.based.table, boxplot.width = 0.3) ## ----eval=TRUE, message=FALSE, warning=FALSE, results='markup'----------- gene.based.table.fdr <- makeGeneTable(featureBasedData, stat = "fdr") lrTestBias(gene.based.table.fdr, boxplot.width = 0.3) ## ----eval=TRUE,warning=FALSE,message=FALSE,results='markup'-------------- result.adjusted <- runPathwaySplice(genewise.table = gene.based.table.fdr, genome = "hg19", id = "ensGene", test.cats = c("GO:BP"), go.size.limit = c(5, 30), method = "Wallenius", use.genes.without.cat = TRUE) head(result.adjusted) ## ----eval=TRUE, warning=FALSE,message=FALSE,results ='markup', fig.align='right', fig.height=13, fig.width=15---- enmap <- enrichmentMap(pathway.res = result.adjusted, n = 7, output.file.dir = tempdir(), similarity.threshold = 0.5, scaling.factor = 2) ## ----eval=FALSE, message = FALSE, warning=FALSE, fig.show='hide'--------- # dir.name <- system.file("extdata", package = "PathwaySplice") # hallmark.local.pathways <- file.path(dir.name, "h.all.v6.0.symbols.gmt.txt") # hlp <- gmtGene2Cat(hallmark.local.pathways, genomeID = "hg19") # # result.hallmark <- runPathwaySplice(genewise.table = gene.based.table.fdr, # genome = "hg19", # id = "ensGene", # gene2cat = hlp, # go.size.limit = c(5, 100), # method = "Wallenius", # binsize = 20, # use.genes.without.cat = TRUE) ## ----eval=FALSE, message=FALSE, warning=FALSE,results='markup',fig.show='hide'---- # # outKegg2Gmt("hsa", file.path(dir.name, "kegg.gmt.txt")) # # kegg.pathways <- gmtGene2Cat(file.path(dir.name, "kegg.gmt.txt"), # genomeID = "hg19") # # result.kegg <- runPathwaySplice(genewise.table = gene.based.table.fdr, # genome = "hg19", # id = "ensGene", # gene2cat = kegg.pathways, # go.size.limit = c(5, 100), # method = "Wallenius", # use.genes.without.cat = TRUE) # ## ----eval=FALSE---------------------------------------------------------- # dir <- system.file("extdata", package="PathwaySplice") # all.gene.table <- readRDS(file.path(dir, "AllGeneTable.rds")) ## ----eval=FALSE, warning=FALSE, message=FALSE, results='markup', fig.show='hide'---- # res.adj <- runPathwaySplice(genewise.table = all.gene.table, # genome = "hg19", # id = "ensGene", # test.cats = "GO:BP", # go.size.limit = c(5, 30), # method = "Wallenius") # # res.unadj <- runPathwaySplice(genewise.table = all.gene.table, # genome = "hg19", # id = "ensGene", # test.cats = "GO:BP", # go.size.limit = c(5, 30), # method = "Hypergeometric") # compareResults(n.go = 20, # adjusted = res.adj, # unadjusted = res.unadj, # gene.based.table = all.gene.table, # output.dir = tempdir(), # type.boxplot = "Only3") ## ----eval=FALSE,warning=FALSE,message=FALSE,results='markup'------------- # PathwaySplice:::compareResults2(result.hyper, # result.Wall, # result.Sampling, # result.Sampling.200k) #