Metadata management for multiomic specification of transcriptional regulatory networks


[Up] [Top]

Documentation for package ‘TxRegInfra’ version 1.0.1

Help Pages

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
dgf_meta dgf_meta: metadata about a small collection of bed files for demonstrating TxRegInfra
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
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
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