## ----style, echo = FALSE, results = 'asis'------------------------------- BiocStyle::markdown() ## ----lkone--------------------------------------------------------------- suppressPackageStartupMessages(library(geuvStore2)) prst = makeGeuvStore2() prst ## ----lktwo,cache=TRUE---------------------------------------------------- library(gQTLBase) # prstore = ciseStore(prst, addProbeMap=TRUE, addRangeMap=TRUE) prstore = makeGeuvStore2() prstore ## ----lookup1------------------------------------------------------------- head( extractByProbes(prstore, probeids=c("ENSG00000183814.10", "ENSG00000174827.9")) ) ## ----lookup2------------------------------------------------------------- head( extractByRanges(prstore, GRanges("1", IRanges(146000000, width=1e6))) ) ## ----doapp--------------------------------------------------------------- lens = storeApply(prstore, length) summary(unlist(lens)) ## ----basecode,eval=FALSE------------------------------------------------- # library(geuvPack) # data(geuFPKM) # seqlevelsStyle(geuFPKM) = "NCBI" # library(GenomeInfoDb) # ok = which(seqnames(geuFPKM) %in% c(1:22, "X")) # geuFPKM = geuFPKM[ok,] # # library(gQTLBase) # #load("../INTERACTIVE/geuvExtractStore.rda") # #kpp = geuvExtractStore@probemap[,1] # data("kpp", package="geuvStore2") # geuFPKM = geuFPKM[kpp,] # # library(gQTLBase) # featlist = balancedFeatList( geuFPKM[order(rowRanges(geuFPKM)),], max=6 ) # lens = sapply(featlist,length) # featlist = featlist[ which(lens>0) ] # # library(BatchJobs) # regExtrP6 = makeRegistry("extractP6pop", # tile/cis # packages=c("GenomicRanges", "gQTLstats", "geuvPack", # "Rsamtools", "VariantAnnotation"), seed=1234) # myf = function(i) { # if (!exists("geuFPKM")) data(geuFPKM) # seqlevelsStyle(geuFPKM) = "NCBI" # curse = geuFPKM[i,] # load("gsvs.rda") # svmat = gsvs$sv # colnames(svmat) = paste0("SV", 1:ncol(svmat)) # colData(curse) = cbind(colData(curse), DataFrame(svmat)) # fmla = as.formula(paste("~popcode+", paste0(colnames(svmat), collapse="+"))) # curse = regressOut(curse, fmla) # pn = gtpath( paste0("chr", as.character(seqnames(curse)[1])) ) # tf = TabixFile(pn) # cisAssoc( curse, tf, cisradius=1000000, nperm=6 ) # } # batchMap(regExtrP6, myf, featlist ) # submitJobs(regExtrP6, job.delay = function(n,i) runif(1,1,3))