## ----style, echo = FALSE, results = 'asis'-------------------------------
BiocStyle::markdown()

## ----lkone---------------------------------------------------------------
suppressPackageStartupMessages(library(geuvStore))
prst = partialRegistry()
prst

## ----lktwo,cache=TRUE----------------------------------------------------
library(gQTLBase)
# prstore = ciseStore(prst, addProbeMap=TRUE, addRangeMap=TRUE)
prstore = makeGeuvStore()
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))

## ----echo=FALSE,eval=FALSE-----------------------------------------------
#  # /udd/stvjc/VM/GEUVADIS/SEPT_2014/FLAT_1M/CHANNING_SGE/newflat.R
#  
#  library(BatchJobs)
#  
#  gtpath = function (chrdigit, useS3 = FALSE)
#  {
#      tmplate = "/proj/rerefs/reref00/EBI/GEUVADIS/VCF/GEUVADIS.chr%%N%%.PH1PH2_465.IMPFRQFILT_BIALLELIC_PH.annotv2.genotypes.vcf.gz"
#      if (useS3)
#          tmplate = "http://1000genomes.s3.amazonaws.com/release/20110521/ALL.chr%%N%%.phase1_release_v3.20101123.snps_indels_svs.genotypes.vcf.gz"
#      gsub("%%N%%", chrdigit, tmplate)
#  }
#  
#  
#  flatReg = makeRegistry("flatReg",  file.dir="flatStore",
#          seed=123, packages=c("GenomicRanges",
#              "GGtools", "VariantAnnotation", "Rsamtools",
#              "geuvPack", "GenomeInfoDb"))
#  
#  
#  
#  chunkGenes = function(chrint, chunk.size=10) {
#    cat(chrint)
#    stopifnot(is(chrint, "integer"))
#    library(geuvPack)
#    if (!exists("geuFPKM")) data(geuFPKM)
#    seqlevelsStyle(geuFPKM) = "NCBI"  # snps indexed this way too
#    curgenes = rownames( geuFPKM[ which(seqnames(geuFPKM)==chrint), ] )
#    glist = chunk( curgenes, chunk.size=chunk.size )
#    lapply(glist, function(x) list(chr=chrint, genes=x) )
#  }
#  
#  gettests = function( chunk, useS3=FALSE ) {
#    library(VariantAnnotation)
#    snpsp = gtpath( chunk$chr, useS3=useS3)
#    tf = TabixFile( snpsp )
#    library(geuvPack)
#    if (!exists("geuFPKM")) data(geuFPKM)
#    seqlevelsStyle(geuFPKM) = "NCBI"
#    clipped = clipPCs(regressOut(geuFPKM, ~popcode), 1:10)
#    set.seed(54321)
#    ans = cisAssoc( clipped[ chunk$genes, ], tf, cisradius=1000000, lbmaf=0.01 )
#    metadata(ans)$prepString = "clipPCs(regressOut(geuFPKM, ~popcode), 1:10)"
#    ans
#    }
#  
#  autosomes = as.integer(1:22)
#  genechunks = lapply(autosomes, chunkGenes, chunk.size=10)
#  
#  flatlist = unlist(genechunks, recursive=FALSE)
#  
#  batchMap(flatReg, gettests, flatlist)
#  
#  submitJobs(flatReg, 1:2)
#