## ----style, echo = FALSE, results = 'asis'------------------------------- BiocStyle::markdown() ## ----lktt,echo=FALSE----------------------------------------------------- litt = structure(c(15280L, 4853L, 1450L, 1153L, 476L, 114L), .Dim = 6L, .Dimnames = structure(list( c("protein_coding", "pseudogene", "antisense", "lincRNA", "processed_transcript", "IG_V_gene")), .Names = "") ) litt ## ----eval=FALSE---------------------------------------------------------- ## gettests = function( chunk, useS3=FALSE ) { ## library(VariantAnnotation) ## snpsp = gtpath( chunk$chr, useS3=useS3) ## tf = TabixFile( snpsp ) ## library(geuvPack) ## if (!exists("geuFPKM")) data(geuFPKM) ## clipped = clipPCs(regressOut(geuFPKM, ~popcode), 1:10) ## set.seed(54321) ## ans = cisAssoc( clipped[ chunk$genes, ], tf, cisradius=1000000, lbmaf=0.01 ) ## metadata(ans)$prepString = "clipPCs(regressOut(geuFPKM, ~popcode), 1:10)" ## ans ## } ## ----bjreg,eval=FALSE---------------------------------------------------- ## flatReg = makeRegistry("flatReg", file.dir="flatStore", ## seed=123, packages=c("GenomicRanges", ## "GGtools", "VariantAnnotation", "Rsamtools", ## "geuvPack", "GenomeInfoDb")) ## ----dosub,eval=FALSE---------------------------------------------------- ## batchMap(flatReg, gettests, flatlist) ## submitJobs(flatReg) ## ----getstuff,results="hide", echo=FALSE--------------------------------- suppressPackageStartupMessages({ library(BiocGenerics) library(Homo.sapiens) library(stats4) library(IRanges) library(GGtools) library(gQTLBase) library(geuvStore2) options(BBmisc.ProgressBar.style="off") }) ## ----doone--------------------------------------------------------------- library(gQTLBase) library(geuvStore2) mm = makeGeuvStore2() mm ## ----getr---------------------------------------------------------------- loadResult(mm@reg, 1)[1:3] ## ----setuplen------------------------------------------------------------ library(BiocParallel) library(parallel) mp = MulticoreParam(workers=max(c(1, detectCores()-4))) register(mp) ## ----getlen, cache=TRUE-------------------------------------------------- lens = storeApply(mm, length) summary(unlist(lens)) ## ----doex,cache=TRUE----------------------------------------------------- pvec = mm@probemap[1:4,1] # don't want API for map, just getting examples litex = extractByProbes( mm, pvec ) length(litex) litex[1:3] ## ----getfff-------------------------------------------------------------- allassoc = storeToFf(mm, "chisq") length(allassoc) object.size(allassoc) allassoc[1:4]