QUALIFIER (version 1.16.1)

qaPreprocess: Preprocessing for QA check

Description

A convenient wrapper that does saveToDB, getQAStats in one call

Usage

qaPreprocess(db = .db, gs, gs.name = "default gatingSet", metaFile, fcs.colname = "name", date.colname = NULL, date.format = "%m/%d/%y", ...)

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.

...

other arguments passed to getQAStats

Value

a list of elements stored in the data environment.

Examples

## Not run: 
# #prepare the data environment
# db<-new.env()
# initDB(db)
# 
# qaPreprocess(db=db,gs=G
# 			,metaFile=metaFile
# 			,fcs.colname="FCS_Files"
# 			,date.colname=c("RecdDt","AnalysisDt")
# 			)
# 
# ## End(Not run)