qaPreprocess {QUALIFIER} | R Documentation |
A convenient wrapper that does saveToDB, getQAStats in one call
qaPreprocess(db = .db, gs, gs.name = "default gatingSet", metaFile, fcs.colname = "name", date.colname = NULL, date.format = "%m/%d/%y", ...)
db |
An |
gs |
A |
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 |
a list of elements stored in the data environment.
## 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)