## ----setup, echo=FALSE, results="hide"------------------------------------- library(TxRegInfra) ## ----lkshi----------------------------------------------------------------- cm = TxRegInfra:::basicCfieldsMap() cmdf = as.data.frame(cm) names(cmdf) = names(cm) cmdf ## ----makecon--------------------------------------------------------------- con1 = mongo(url=URL_txregInAWS(), db="txregnet") cd = TxRegInfra::basicColData rme0 = RaggedMongoExpt(con1, colData=cd) rme0 ## ----lkcon1---------------------------------------------------------------- mycon = mongo(db="txregnet", url=URL_txregInAWS(), # ATLAS deployment in AWS collection="Lung_allpairs_v7_eQTL") mycon$find(q=rjson::toJSON(list(chr=17)), limit=2) ## ----dosb------------------------------------------------------------------ lname_eqtl = "Lung_allpairs_v7_eQTL" lname_dhs = "ENCFF001SSA_hg19_HS" # see dnmeta lname_fp = "fLung_DS14724_hg19_FP" si17 = GenomeInfoDb::Seqinfo(genome="hg19")["chr17"] si17n = si17 GenomeInfoDb::seqlevelsStyle(si17n) = "NCBI" s1 = sbov(rme0[,lname_eqtl], GRanges("17", IRanges(38.06e6, 38.15e6), seqinfo=si17n)) s2 = sbov(rme0[,lname_dhs], GRanges("chr17", IRanges(38.06e6, 38.15e6), seqinfo=si17)) s3 = sbov(rme0[,lname_fp], GRanges("chr17", IRanges(38.06e6, 38.15e6), seqinfo=si17))