sbov: prototype of subsetter for mongo resource

In vjcitn/TxRegInfra2: Metadata management for multiomic specification of transcriptional regulatory networks, version 2

Description

prototype of subsetter for mongo resource

Usage

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

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
simplify	logical(1) if TRUE, a GRanges is assembled; if FALSE, a RaggedExperiment is returned

Value

if simplify is TRUE (the default), a GRanges is returned with assay components in the mcols; otherwise a RaggedExperiment instance, with metadata component 'docType' set to propagate the input type

Note

This is a placeholder for a proper subsetByOverlaps method. While it would appear sensible to allow subsetting for diverse assay types (e.g., eQTL, FP), in version 1.5.x this is not supported. Each call can operate on only one sample type.

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_txregLocal(), db='txregnet')
 #cd = makeColData(url=URL_txregLocal(), db='txregnet')
 cd = TxRegInfra2::basicColData.tiny
 rme1 = RaggedMongoExpt(m1, cd[which(cd$type=='FP'),])
 BiocParallel::register(BiocParallel::SerialParam())
 qrng = GRanges('chr1', IRanges(1e6, 1.5e6))
 GenomeInfoDb::genome(qrng) = "hg19"
 ss = sbov(rme1, GRanges('chr1', IRanges(1e6, 1.5e6)), simplify=FALSE)
} 

vjcitn/TxRegInfra2 documentation built on Jan. 1, 2021, 12:41 p.m.