qaPreprocess {QUALIFIER} | R Documentation

## 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)

[Package QUALIFIER version 1.29.1 Index]