importBedToMongo: arrange import to mongo using mongoimport, setting up type...

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

Description

arrange import to mongo using mongoimport, setting up type and fields appropriately

Usage

importBedToMongo(
  path,
  collectionName,
  bedType = "narrowPeak",
  dbname = "db",
  importCmd = "mongoimport",
  host = "127.0.0.1"
)

Arguments

path	path to bed file (not compressed)
collectionName	name to use in mongodb
bedType	one of 'narrowPeak', 'broadPeak', 'chromHMM': contact developers for other types if desired
dbname	mongodb database name, used directly with system2('mongoimort ...')
importCmd	how to invoke 'mongoimport', default is to assume it can be found in PATH
host	host identifier for mongoimport, defaults to 127.0.0.1

Value

if error encountered, return the try-error content, otherwise TRUE

Examples

f1 = dir(system.file('bedfiles', package='TxRegInfra2'), full=TRUE, patt='ENCFF971VCD')
f2 = dir(system.file('bedfiles', package='TxRegInfra2'), full=TRUE, patt='E096_imp12')
if (verifyHasMongoCmd('mongoimport')) {
chk1 = importBedToMongo(f1, 'vjc1', db='txregnet')
stopifnot(chk1)
chk2 = importBedToMongo(f2, 'vjc2', db='txregnet', bedType='chromHMM')
stopifnot(chk2)
system2("mongo", args=c("txregnet", "--eval", "'db.vjc1.remove({})'")) 
system2("mongo", args=c("txregnet", "--eval", "'db.vjc2.remove({})'"))
}

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