qaPreprocess: Preprocessing for QA check

In QUALIFIER: Quality Control of Gated Flow Cytometry Experiments

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)

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