makeAggregator: generate JSON to aggregate (counting records, and, by...

In TxRegInfra: Metadata management for multiomic specification of transcriptional regulatory networks

Description

generate JSON to aggregate (counting records, and, by default, averaging a given variable) within a collection

Usage

makeAggregator(by = "chrom", vbl = "chromStart", opname = "average",
  op = "$avg")

Arguments

by	character(1) telling the field for stratifying records for aggregation
vbl	character(1) telling field with numerical value for which a statistic will be computed within strata defined by 'by'
opname	character(1) define the name of the aggregation
op	character(1) evaluating to a mongo aggregation operator like '$avg' or '$min'

Value

a JSON document as produced by rjson::toJSON

Note

This produces json that can be used as an argument to m$aggregate() for m a mongolite::mongo instance

Examples

makeAggregator()
if (interactive() & verifyHasMongoCmd()) {
   remURL = URL_txregInAWS()
   colls = listAllCollections( url=remURL, db = 'txregnet')
   m1 = mongo(url = remURL, db = 'txregnet', 
     collection='CD14_DS17215_hg19_FP')
# find minimum value of statistic 'stat' per chromosome
   newagg = makeAggregator( by='chr',
     vbl='stat', op='$min', opname='min')
   tab = m1$aggregate( newagg )
   head(tab)
   }

TxRegInfra documentation built on Nov. 8, 2020, 5:15 p.m.