# Metadata management for multiomic specification of transcriptional regulatory networks

## Documentation for package ‘TxRegInfra’ version 1.8.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

addsyms | add gene symbols to a GRanges that uses ensembl identifiers
basicColData | basicColData: metadata about a small collection of files for demonstrating TxRegInfra
basicFormatter | operate on a character vector to derive a DataFrame, splitting on a tokenand retrieving first and last split fragments as 'base' and 'type' fields
demo_eQTL_granges | a GRanges instance with eQTL metadata returned by 'sbov'
demo_fimo_granges | a list of GRanges instances with TF FIMO scores returned by 'fimo_granges'
dgf_meta | dgf_meta: metadata about a small collection of bed files for demonstrating TxRegInfra
dnmeta | metadata about DNaseI hotspots from ENCODE
dnmetaApp | support search of hotspot/peak data from ENCODE
getDocumentFields | determine the fields present in a txregnet document
getFieldNames | get names of fields in a collection in remote txregnet
grConverter | convert a GRanges to a JSON query for mongodb
importBedToMongo | arrange import to mongo using mongoimport, setting up type and fields appropriately
listAllCollections | list all collections in a database, using command-line interface
makeAggregator | generate JSON to aggregate (counting records, and, by default, averaging a given variable) within a collection
makeColData | generate a colData component corresponding to a mongodb
makeGRConverterList | generate a list of GRanges to JSON for queries to mongo
oldbasicColData | oldbasicColData: metadata about a small collection of files for demonstrating TxRegInfra
ragged41FP | ragged41FP: A RaggedExperiment instance with digital genomic footprints over the coding region of ORMDL3
RaggedMongoExpt | bind colData to a mongo-based ragged-experiment incubator
sbov | prototype of subsetter for mongo resource
sbov_output_eQTL | a GRanges instance with eQTL metadata returned by 'sbov'
sbov_output_FP | a GRanges instance with digital genomic footprint metadata returned by 'sbov'
sbov_output_HS | a GRanges instance with DnaseI hotspot metadata returned by 'sbov'
sbov_to_graphNEL | convert sbov() output to annotated graphNEL
txmodels | use Gviz to render transcript models via GeneRegionTrack, but keep lightweight through requireNamespace and suggestion for installation
txregCollections | list collections in AWS mongo server for txregnet
URL_txregInAWS | return mongodb URL for working mongo server
URL_txregLocal | local mongodb txregnet
verifyHasMongoCmd | check for existence of 'mongo' command, for db.getCollectionNames etc.
verifyRunningMongodb | check for accessible local mongodb