matchRecords: matchRecords

In SOLV-Code/sdsynopsis: Salmon data extraction and summary

Description

Function to match records across databases. Generates various outputs (rosetta files, mismatch tracking). Target folders are generated if they don't exist

Usage

matchRecords(
  nuseds.rds.file,
  nuseds.pop.info,
  epad.rds.file,
  mrp.rds.file,
  mrp.rds.details.file,
  out.folder = "OUTPUT",
  tracking.folder = "DATA/TrackingFiles",
  lookup.folder = "DATA/LookupFiles",
  processed.folder = "DATA/LargeFiles_Processed"
)

Arguments

nuseds.rds.file	path to the nuSEDS input file (in RDS format)
nuseds.pop.info	path to the pop/site info file from nuSEDS (in csv format)
epad.rds.file	path to the EPAD input file (in RDS format)
mrp.rds.file	path to the MRP summary input file (in RDS format)
out.folder	path for storing output (CU summary stored there)
tracking.folder	path for storing tracking files (site mismatches etc. stored there)
lookup.folder	path for storing generated lookup files ("rosetta" files stored there)
processed.folder	folder path for storing modified csv files (MRP summaries with CU match stored there)
epad.rds.details.file	path to the EPAD details input file (in RDS format)

Examples

## Not run: matchRecords(nuseds.rds.file = "DATA/RDSFiles/nuSEDS.RDS",
            nuseds.pop.info ="DATA/LookupFiles/aopen-data-portaljanuary-2019conservation_unit_system_sites.csv",
           epad.rds.file =  "DATA/RDSFiles/EPAD.RDS",
           mrp.rds.file = "DATA/RDSFiles/MRP.RDS" )
## End(Not run)

SOLV-Code/sdsynopsis documentation built on April 29, 2020, 5:20 p.m.