saveToDB: Save the gating set and annotation data into the data...

In QUALIFIER: Quality Control of Gated Flow Cytometry Experiments

Description

Save the gating set and annotation data into the data environment.

Usage

saveToDB(db = .db, gs, gs.name = "default gatingSet", metaFile,
  fcs.colname = "name", date.colname = NULL, date.format)

Arguments

db	An environment storing all the QA data. By default it is an hidden global environment .db.
gs	A GatingSet containing multiple gating hierarchies
gs.name	A character scalar giving the name of the GatingSet.
metaFile	A character scalar giving the file path of the sample annotation data, which is a csv spreadsheet contains the meta information. Each row corresponds to one FCS file and The QUALIFIER package looks for the FCS filename from "name" column of the spreadsheet.
fcs.colname	A character scalar indicating column name that specify FCS file names in annotation data.
date.colname	A character scalar indicating column names that contains date information which are automatically formatted to date object in R
date.format	A character scalar indicating the format of date column , default is "%m/%d/%y".. see as.Date for more details.

Value

An unique id for GatingSet that is generated incrementally.

Examples

## Not run: 
#prepare the data environment
db<-new.env()
initDB(db)

metaFile="~/rglab/workspace/QUALIFIER/misc/ITN029ST/FCS_File_mapping.csv"
##append the annotation  and Gating set to db
metaFile<-"FCS_File_mapping.csv"
saveToDB(db=db,gs=G
	,metaFile=metaFile
	,fcs.colname="FCS_Files"
	,date.colname=c("RecdDt","AnalysisDt")
) 


## End(Not run)

QUALIFIER documentation built on Oct. 31, 2019, 3:24 a.m.