## ----loadPackage-QUALIFIER, echo=FALSE,results='hide', message=FALSE----- library(QUALIFIER) QUALIFIER:::qa.par.set("idCol","id") QUALIFIER:::qa.par.get("idCol") ## ----parseWorkspace, eval=FALSE, echo=TRUE,results='markup'-------------- # ws<-openWorkspace("./data/QA_MFI_RBC_bounary_eventsV3.xml")##should replace with your own xml workspace file path # GT<-parseWorkspace(ws,execute=FALSE,useInternal=TRUE) ## ----gh_template1, eval=FALSE, echo=TRUE,results='markup'---------------- # gh_template<-GT[[1]] ## ----gh_template2, eval=FALSE, echo=TRUE,results='markup'---------------- # ##datapath is the path where FCS files stores # G<-GatingSet(gh_template,filenames,path="./data") # getPopStats(G[[1]]) ## ----getQAStats, eval=FALSE ,echo=TRUE, results='markup'----------------- # db<-new.env() # initDB(db) # qaPreprocess(db=db,gs=G # ,metaFile="./data/FCS_File_mapping.csv" #should replace with your own FCS meta data file path # ,fcs.colname="FCS_Files" # ,date.colname=c("RecdDt","AnalysisDt") # ) ## ----loadData, echo=FALSE, results='hide'-------------------------------- data("ITNQASTUDY") ## ----read.qaTask, echo=TRUE, results='markup'---------------------------- checkListFile<-file.path(system.file("data",package="QUALIFIER"),"qaCheckList.csv.gz") qaTask.list<-read.qaTask(db,checkListFile=checkListFile) qaTask.list[1:2] ## ----qaTask-RBCLysis, results='markup'----------------------------------- qaTask.list[["RBCLysis"]] ## ----qaCheck-RBCLysis, results='markup'---------------------------------- qaCheck(qaTask.list[["RBCLysis"]] ,outlierfunc=list(func = outlier.cutoff ,args = list(lBound=0.8) ) ) ## ----plot-RBCLysis, results='markup'------------------------------------- plot(qaTask.list[["RBCLysis"]],xlab="Record Date",ylab="percent") ## ----plot-RBCLysis-subset, results='markup'------------------------------ plot(qaTask.list[["RBCLysis"]],subset=Tube=='CD8/CD25/CD4/CD3/CD62L',xlab="Record Date",ylab="percent") ## ----clearCheck,results='markup'----------------------------------------- clearCheck(qaTask.list[["RBCLysis"]]) ## ----plot-RBCLysis-subset2, results='markup',eval=FALSE------------------ # plot(qaTask.list[["RBCLysis"]],subset=name=='06087181_F01_I010.fcs',scatterPlot=TRUE) ## ----qaTask-MNC, results='markup'--------------------------------------- qaTask.list[["MNC"]] ## ----qaCheck-MNC, results='markup'-------------------------------------- qaCheck(qaTask.list[["MNC"]],z.cutoff=1.5) ## ----plot-MNC, results='markup'------------------------------------------ plot(qaTask.list[["MNC"]],proportion~factor(coresampleid),xlab="Sample ID",ylab="percent",scales=list(x=list(rot=45))) ## ----plot-MNC-scatter, results='markup',eval=FALSE----------------------- # # plot(qaTask.list[["MNC"]] # ,scatterPlot=TRUE # ,subset=coresampleid==11730) ## ----qaTask-BoundaryEvents, results='markup'----------------------------- qaTask.list[["BoundaryEvents"]] ## ----qaCheck-BoundaryEvents, results='markup'--------------------------- qaCheck(qaTask.list[["BoundaryEvents"]] ,sum(proportion) ~ RecdDt | name ,outlierfunc=list(func = outlier.cutoff ,args =list(uBound=0.0003) ) ) ## ----plot-BoundaryEvents, results='markup'------------------------------- plot(qaTask.list[["BoundaryEvents"]],proportion ~ RecdDt | channel,xlab="Record Date",ylab="percent") ## ----qaCheck-MFIOverTime, results='markup'------------------------------- qaCheck(qaTask.list[["MFIOverTime"]] ,rFunc= list (func = rlm ,args = list(z.cutoff=3) ) ) plot(qaTask.list[["MFIOverTime"]] ,y=MFI~RecdDt|stain ,subset=channel%in%c('FITC-A') ,rFunc=rlm ,scales=list(y=c(relation="free")) ,xlab="Record Date" ) ## ----plot-spike, results='markup'---------------------------------------- qaCheck(qaTask.list[["spike"]] ,outlierfunc = list (func = outlier.t ,args = list(alpha=0.00001) ) ) plot(qaTask.list[["spike"]],y=spike~RecdDt|channel ,subset=Tube=='CD8/CD25/CD4/CD3/CD62L'&channel%in%c('FITC-A') ,xlab="Record Date" ) ## ----tubesEvents1, results='hide',echo=FALSE----------------------------- tubesEvents <- read.csv(file.path(system.file("data",package="QUALIFIER"),"tubesevents.csv.gz"),row.names=1) tubesEvents <- QUALIFIER:::.TubeNameMapping(db,tubesEvents=tubesEvents[,3,drop=F]) ## ----tubesEvents2, results='markup'-------------------------------------- tubesEvents ## ----plot-NumberOfEvents, results='markup'------------------------------- qaCheck(qaTask.list[["NumberOfEvents"]] ,formula=count ~ RecdDt | Tube ,outlierfunc = list(func = outlier.cutoff ,args = list(lBound = 0.8 * tubesEvents) ) ) plot(qaTask.list[["NumberOfEvents"]] ,subset=Tube=='CD8/CD25/CD4/CD3/CD62L' ,xlab="Record Date" ,ylab="Cell counts" ) ## ----plot-RedundantStain, results='markup'------------------------------- qaCheck(qaTask.list[["RedundantStain"]] ,gOutlierfunc = list(func = outlier.norm , args =list(z.cutoff = 1) ) ) plot(qaTask.list[["RedundantStain"]] ,y=proportion~factor(coresampleid)|channel:stain ,subset=stain%in%c('CD8') ,scales=list(x=list(cex=0.5,rot=45)) ,xlab="Sample ID" ,ylab="percent" ) ## ----qa.report1,eval=FALSE, echo=TRUE, results='markup'------------------ # qaReport(qaTask.list # ,outDir="~/temp" # ,plotAll=FALSE # ,subset=as.POSIXlt(RecdDt)$year==(2007-1900) # ) # ## ----qa.report2,eval=FALSE, echo=TRUE, results='markup'------------------ # htmlReport(qaTask.list[["MFIOverTime"]])<-TRUE # rFunc(qaTask.list[["MFIOverTime"]])<-rlm # scatterPar(qaTask.list[["MFIOverTime"]])<-list(xlog=TRUE) # scatterPar(qaTask.list[["BoundaryEvents"]])<-list(xlog=TRUE) # scatterPar(qaTask.list[["RedundantStain"]])<-list(xlog=TRUE) # qpar(qaTask.list[["RedundantStain"]])<-list(scales=list(x=list(relation="free")))