| sbov {TxRegInfra} | R Documentation |
prototype of subsetter for mongo resource
sbov(rme, gr, map = basicCfieldsMap(), docTypeName = "type")
rme |
RaggedMongoExpt instance |
gr |
GRanges instance to subset by |
map |
list with one element per document type telling what fields are chr, start, stop |
docTypeName |
character(1) naming column of colData(rme) that has document type |
a RaggedExperiment instance
requireNamespace('mongolite')
if (verifyHasMongoCmd()) { # for makeColData, which must be able to enumerate collections,
# and thus must be able to run system (as opposed to mongolite function) 'mongo'
m1 = mongolite::mongo(url=URL_txregInAWS(), db='txregnet')
cd = makeColData(url=URL_txregInAWS(), db='txregnet')
rme1 = RaggedMongoExpt(m1, cd[which(cd$type=='FP'),][seq_len(8),])
BiocParallel::register(BiocParallel::SerialParam())
ss = sbov(rme1, GRanges('chr1', IRanges(1e6, 1.5e6)))
}