## ----setup,message=FALSE, eval=FALSE------------------------------------------
#  library(BiocHail)

## ----getukbb, eval=FALSE------------------------------------------------------
#  hl = hail_init()
#  ss = get_ukbb_sumstat_10kloci_mt(hl) # can take about a minute to unzip 5GB
#  ss$count()   # but if a persistent MatrixTable is at the location given
#               # by env var HAIL_UKBB_SUMSTAT_10K_PATH it goes quickly

## ----lkba, eval=FALSE---------------------------------------------------------
#  hl = bare_hail()
#  hl$init(idempotent=TRUE, spark_conf=list(
#    'spark.hadoop.fs.gs.requester.pays.mode'= 'CUSTOM',
#    'spark.hadoop.fs.gs.requester.pays.buckets'= 'ukb-diverse-pops-public',
#    'spark.hadoop.fs.gs.requester.pays.project.id'= Sys.getenv("GOOGLE_PROJECT")))

## ----lkss, eval=FALSE---------------------------------------------------------
#  sscol = ss$cols()$collect() # OK because we are just working over column metadata
#  ss1 = sscol[[1]]
#  names(ss1)
#  ss1$get("phenocode")
#  ss1$get("description")

## ----lkmul, eval=FALSE--------------------------------------------------------
#  multipop_df(ss1)

## ----dodt, message=FALSE, eval=FALSE------------------------------------------
#  library(DT)
#  ndf = do.call(rbind, lapply(sscol[1:10], multipop_df))
#  datatable(ndf)

## ----dotrim, eval=FALSE-------------------------------------------------------
#  sss = ss$sample_rows(.01)$sample_cols(.01)
#  sss$count()

## ----getrm, eval=FALSE--------------------------------------------------------
#  rss = sss$rows()$collect()
#  rss1 = rss[[1]]
#  names(rss1)
#  names(rss1$locus)
#  rss1$locus$contig
#  sapply(c("contig", "position"), function(x) rss1$locus[[x]])

## ----getent, eval=FALSE-------------------------------------------------------
#  sse = sss$entries()$collect()
#  length(sse)
#  names(sse[[1]])
#  sse1 = sse[[1]]

## ----lkss11, eval=FALSE-------------------------------------------------------
#  length(sse1$summary_stats)
#  names(sse1$summary_stats[[1]])
#  sse1$summary_stats[[1]]$Pvalue

## ----eval = FALSE-------------------------------------------------------------
#  if (!require("BiocManager"))
#      install.packages("BiocManager")
#  BiocManager::install("BiocHail")

## ----sessionInfo--------------------------------------------------------------
sessionInfo()