sbov {TxRegInfra}R Documentation

prototype of subsetter for mongo resource

Description

prototype of subsetter for mongo resource

Usage

sbov(rme, gr, map = basicCfieldsMap(), docTypeName = "type")

Arguments

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

Value

a RaggedExperiment instance

Examples

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')
 cd = TxRegInfra::basicColData
 rme1 = RaggedMongoExpt(m1, cd[which(cd$type=='FP'),][seq_len(8),])
 BiocParallel::register(BiocParallel::SerialParam())
 ss = sbov(rme1, GRanges('chr1', IRanges(1e6, 1.5e6)))
} 

[Package TxRegInfra version 1.4.0 Index]