Nothing
examples/example.R
In QUALIFIER: Quality Control of Gated Flow Cytometry Experiments
library(QUALIFIER)
#save_db(db, path = "/home/wjiang2/rglab/workspace/QUALIFIER/output/preprocessedData", overwrite = T, cdf = "copy")
db <- load_db(path = "/home/wjiang2/rglab/workspace/QUALIFIER/output/preprocessedData")
qaTask.list <- db$qaTaskList
###############################################################################
#1.parse gating template
###############################################################################
ws<-openWorkspace("/shared/silo_researcher/Gottardo_R/mike_working/ITN029ST/QA_template.xml")
GT<-parseWorkspace(ws
,name=2
,execute=F
,subset=1
)
gh_template<-GT[[1]]
gs_pop_get_count_fast(gh_template)[,2:3]
#test the matchNode
###############################################################################
#2.apply gating template to new data
###############################################################################
datapath<-"/shared/silo_researcher/Gottardo_R/mike_working/ITN029ST/"
#newSamples<-getSample(gh_template)
newSamples<-list.files(datapath)[1:200]
length(newSamples)
G<-GatingSet(gh_template
,newSamples[1:100]
,path=datapath
,isNcdf=T
# ,dMode=4
)
gs_pop_get_count_fast(G[[1]])[,2:3]
plotGate(G[[1]],merge=F)
################################################################################
#3.extract stats (6 min for 500 samples, 12 min for 1k samples)
###############################################################################
#library(parallel)
db<-new.env()
initDB(db)
metaFile="/shared/silo_researcher/Gottardo_R/mike_working/ITN029ST/FCS_File_mapping.csv"
qaPreprocess(db=db,gs=G
,metaFile=metaFile
,fcs.colname="FCS_Files"
,date.colname=c("RecdDt","AnalysisDt")
,nslave=1
# ,type="SOCK"
,isMFI=T,isSpike=T, isChannel = T
)
getQAStats(G[[1]],isMFI=T,isSpike=T)
#colnames(pData(db$gs[[1]]))
#pData(G)
#head(db$stats)
#getQAStats(G[1])
#saveToDB(db=db,gs=G
# ,metaFile=metaFile
# ,fcs.colname="FCS_Files"
# ,date.colname=c("RecdDt","AnalysisDt")
# )
################################################################################
#4.load QA check list
###############################################################################
checkListFile<-file.path(system.file("data",package="QUALIFIER"),"qaCheckList.csv.gz")
qaTask.list <- read.qaTask(db,checkListFile=checkListFile)
pData(db$gs[[1]])$RecdDt<-as.Date(pData(db$gs[[1]])$RecdDt)
QUALIFIER:::.parseTubeID(db)#parse TubeID from FCS filenames
#read pre-determined events number for tubes from csv file
##pannel name should be in place of tube name since the entire package is using pannel name
##to represent the tube
tubesEvents<-read.csv(file.path(system.file("data",package="QUALIFIER"),"tubesevents.csv.gz"),row.names=1)
tubesEventsOrig<-QUALIFIER:::.TubeNameMapping(db,tubesEvents=tubesEvents[,3,drop=F])
tubesEvents20090825<-QUALIFIER:::.TubeNameMapping(db,tubesEvents=tubesEvents[,2,drop=F])
tubesEvents20090622<-QUALIFIER:::.TubeNameMapping(db,tubesEvents=tubesEvents[,1,drop=F])
###80% of the pre-defined the value for each pannel
qaCheck(qaTask.list[["NumberOfEvents"]]
,formula=count ~ RecdDt | Tube
,outlierfunc=list(func=outlier.cutoff,args=list(lBound=0.8*tubesEvents20090825))
,subset=as.Date(RecdDt,"%m/%d/%y")>='2009-08-25'
)
qaCheck(qaTask.list[["NumberOfEvents"]]
,formula=count ~ RecdDt | Tube
,outlierfunc=list(func=outlier.cutoff,args=list(lBound=0.8*tubesEvents20090622))
,subset=as.Date(RecdDt,"%m/%d/%y")<'2009-08-25'&as.Date(RecdDt,"%m/%d/%y")>='2009-06-22'
)
qaCheck(qaTask.list[["NumberOfEvents"]]
,formula=count ~ RecdDt | Tube
,outlierfunc=list(func=outlier.cutoff,args=list(lBound=0.8*tubesEventsOrig))
,subset=as.Date(RecdDt,"%m/%d/%y")<'2009-06-22'
)
CairoX11()
plot(qaTask.list[["NumberOfEvents"]]
# ,count ~ RecdDt
,subset=Tube=='CD8/CD25/CD4/CD3/CD62L'
#,dest="image"
# ,scales=list(x=list(rot=45
# ,cex=0.5
# ))
# ,pch=19
)
#qaTask.list[["NumberOfEvents"]]@formula<-count ~ `RecdDt` | `t/Tube`:`t/PTID`
plot(qaTask.list[["NumberOfEvents"]]
# ,subset=id=='245'
# ,scatterPlot=TRUE
# ,scatterPar=list(stat=T)
)
clearCheck(qaTask.list[["NumberOfEvents"]])
##add new aggregated stats
QUALIFIER:::.addStats(qaTask.list[["BoundaryEvents"]]
,definition=sum(proportion)~RecdDt|fileid+gsid
,pop="/root/MNC/margin"
,statName="sum.prop"
)
head(subset(
queryStats(qaTask.list[["BoundaryEvents"]]
,y=sum.prop ~ RecdDt
,pop="margin"
# ,subset=value>0&id==806
)
,outlier==TRUE)
)
#check on the new stats
qaCheck(qaTask.list[["BoundaryEvents"]]
,sum.prop ~ RecdDt
,outlierfunc= list(func = outlier.cutoff,args=list(uBound=0.0003))
)
plot(qaTask.list[["BoundaryEvents"]]
,sum.prop ~ RecdDt
# ,subset=channel=="PE-A"
# &id==806
# ,ylab="sum(percent)"
# ,scatterPlot=T
# ,scatterPar=list(
# xlog=T
# ,stat=T
# )
,scales=list(format="%m/%d/%y")
# ,plotAll="none"
# ,dest="image"
)
#plot(qaTask.list[["BoundaryEvents"]]
# ,proportion ~ RecdDt|channel
## ,subset=channel=="PE-A"
## &id==806
# ,ylab="percent"
## ,scatterPlot=T
## ,scatterPar=list(
## xlog=T
## ,stat=T
## )
# ,scales=list(format="%m/%d/%y")
### ,plotAll=F
## ,dest="image"
#)
clearCheck(qaTask.list[["BoundaryEvents"]])
qaCheck(qaTask.list[["MFIOverTime"]]
# ,outlierfunc=outlier.norm
,rFunc=rlm
# ,Subset=channel%in%c('PE-Cy7-A')
# ,z.cutoff=10
)
head(subset(
queryStats(qaTask.list[["MFIOverTime"]]
# ,y=sum.prop ~ RecdDt
,pop="MFI"
# ,subset=value>0&id==806
)
,outlier==TRUE)
)
plot(qaTask.list[["MFIOverTime"]]
# ,y=MFI~RecdDt|stain
,subset=channel%in%c('APC-A')
&stain=="CD62L APC-A"
## &id==806
# ,rFunc=rlm
# ,scales=list(format="%m/%d/%y")
## ,scatterPlot=TRUE
# ,scatterPar=list(xlog=F)
# ,dest="image"
)
clearCheck(qaTask.list[["MFIOverTime"]])
qaCheck(qaTask.list[["RBCLysis"]]
,outlierfunc=list(func=outlier.cutoff
,args=list(lBound=0.9))
)
subset(
queryStats(qaTask.list[["RBCLysis"]]
,subset=Tube=='CD8/CD25/CD4/CD3/CD62L')
,outlier==TRUE)
plot(qaTask.list[["RBCLysis"]]
# ,subset=Tube=='CD8/CD25/CD4/CD3/CD62L'
# &id%in%c(270)
# , RecdDt~proportion | Tube
# ,scales=list(format="%m/%d/%y")
# ,ylab="percent"
# ,scatterPlot=T
# ,scatterPar=list(stat=T
# ,xbin=128)
# ,horiz=T
# ,dest="image"
# ,highlight="coresampleid"
# ,plotAll="none"
# ,width=27,height=13
)
clearCheck(qaTask.list[["RBCLysis"]])
qaCheck(qaTask.list[["spike"]]
,outlierfunc = list(func = outlier.t
,args = list(alpha=0.001
,isLower=FALSE)
)
)
plot(qaTask.list[["spike"]]
,y=spike~RecdDt|channel
,subset=Tube=='CD11c/CD80/DUMP/HLADr/CD123'
# ,dest="image"
# ,plotAll=T
)
plot(qaTask.list[["spike"]],y=spike~RecdDt|channel
,subset=channel=='FITC-A'
# &id%in%c(245,119)
# ,scatterPlot=TRUE
,scatterPar=list(ylog=T
,xlim=c(0,100)
# ,xbin=128
)
# ,dest="image"
# ,plotAll="none"
)
qaCheck(qaTask.list[["MNC"]]
# ,Subset=coresampleid%in%c(11730,8780)
# ,z.cutoff=0.1
)
plot(qaTask.list[["MNC"]]
,proportion~`coresampleid`
# , factor(coresampleid)~proportion
# ,par=list(horiz=TRUE)
)
#scatter plot for a sample group
plot(qaTask.list[["MNC"]]
,proportion~factor(coresampleid)
# ,par=list(xlab="coresampleid")
# , coresampleid ~proportion
# ,par=list(horiz=TRUE)
# ,subset=coresampleid%in%c(
## 11730
# 8780
# )
# ,scatterPlot=TRUE
,scatterPar=list(xbin=128
,stat=T)
,dest="~/rglab/workspace/QUALIFIER/output/image"
,plotAll=F
)
#scatter for one sample
plot(qaTask.list[["MNC"]]
,scatterPlot=TRUE
,subset=coresampleid==11730&id==245)
clearCheck(qaTask.list[["MNC"]])
qaCheck(qaTask.list[["RedundantStain"]]
# ,gOutlierfunc=qoutlier
# ,outlierfunc=qoutlier
# ,alpha=1.5
# ,z.cutoff=2
)
##example of passing lattice arguments
plot(qaTask.list[["RedundantStain"]]
,subset=channel=='APC-A'
# &stain%in%c('CD123','CD3')
# &coresampleid==11730
,y=proportion~factor(coresampleid)|channel:stain
# ,scatterPlot=T
,scatterPar=list(xlog=F
,stat=T
)
,scales=list(x=list(relation="free"))
# ,layout=c(2,NA,1)
# ,dest="image"
)
################################################################################
#4.qa report in html format
#set plotAll=TRUE to generate the scatter plots for all the individual FCS files
#otherwise only plots for outliers are generated.
###############################################################################
##customerize some of the task before pass them to report method
htmlReport(qaTask.list[["MFIOverTime"]])<-TRUE
rFunc(qaTask.list[["MFIOverTime"]])<-rlm
highlight(qaTask.list[["BoundaryEvents"]])<-"coresampleid"
#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")))
#modify functions within package namespace
funcToinsert <- ".postProcessSVG"
funcSym <- as.symbol(funcToinsert)
eval(substitute(environment(ff) <- getNamespace("QUALIFIER"), list(ff = funcSym)))
assignInNamespace(funcToinsert, eval(funcSym), ns = "QUALIFIER")
db <- load_db(path = "/home/wjiang2/rglab/workspace/QUALIFIER/output/preprocessedData")
qaTask.list <- db$qaTaskList
db$stats[sid == 3, value:= 0.1]
qaCheck(qaTask.list[["MNC"]]
, gOutlierfunc=list(func=outlier.norm
,args=list(alpha=0.1))
)
plot(qaTask.list[["MNC"]]
# , dest = "rglab/workspace/QUALIFIER/output/image"
# , plotAll = "none"
# , scatterPlot = T
# , subset = participantid == "002005"
# , scatterPar = list(xbin = 32)
)
qaReport(qaTask.list, outDir = "rglab/workspace/QUALIFIER/output/"
, plotAll = T
, subset = participantid == "002005"
)
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QUALIFIER documentation built on Oct. 31, 2019, 3:24 a.m.
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library(QUALIFIER)
#save_db(db, path = "/home/wjiang2/rglab/workspace/QUALIFIER/output/preprocessedData", overwrite = T, cdf = "copy")
db <- load_db(path = "/home/wjiang2/rglab/workspace/QUALIFIER/output/preprocessedData")
qaTask.list <- db$qaTaskList
###############################################################################
#1.parse gating template
###############################################################################
ws<-openWorkspace("/shared/silo_researcher/Gottardo_R/mike_working/ITN029ST/QA_template.xml")
GT<-parseWorkspace(ws
,name=2
,execute=F
,subset=1
)
gh_template<-GT[[1]]
gs_pop_get_count_fast(gh_template)[,2:3]
#test the matchNode
###############################################################################
#2.apply gating template to new data
###############################################################################
datapath<-"/shared/silo_researcher/Gottardo_R/mike_working/ITN029ST/"
#newSamples<-getSample(gh_template)
newSamples<-list.files(datapath)[1:200]
length(newSamples)
G<-GatingSet(gh_template
,newSamples[1:100]
,path=datapath
,isNcdf=T
# ,dMode=4
)
gs_pop_get_count_fast(G[[1]])[,2:3]
plotGate(G[[1]],merge=F)
################################################################################
#3.extract stats (6 min for 500 samples, 12 min for 1k samples)
###############################################################################
#library(parallel)
db<-new.env()
initDB(db)
metaFile="/shared/silo_researcher/Gottardo_R/mike_working/ITN029ST/FCS_File_mapping.csv"
qaPreprocess(db=db,gs=G
,metaFile=metaFile
,fcs.colname="FCS_Files"
,date.colname=c("RecdDt","AnalysisDt")
,nslave=1
# ,type="SOCK"
,isMFI=T,isSpike=T, isChannel = T
)
getQAStats(G[[1]],isMFI=T,isSpike=T)
#colnames(pData(db$gs[[1]]))
#pData(G)
#head(db$stats)
#getQAStats(G[1])
#saveToDB(db=db,gs=G
# ,metaFile=metaFile
# ,fcs.colname="FCS_Files"
# ,date.colname=c("RecdDt","AnalysisDt")
# )
################################################################################
#4.load QA check list
###############################################################################
checkListFile<-file.path(system.file("data",package="QUALIFIER"),"qaCheckList.csv.gz")
qaTask.list <- read.qaTask(db,checkListFile=checkListFile)
pData(db$gs[[1]])$RecdDt<-as.Date(pData(db$gs[[1]])$RecdDt)
QUALIFIER:::.parseTubeID(db)#parse TubeID from FCS filenames
#read pre-determined events number for tubes from csv file
##pannel name should be in place of tube name since the entire package is using pannel name
##to represent the tube
tubesEvents<-read.csv(file.path(system.file("data",package="QUALIFIER"),"tubesevents.csv.gz"),row.names=1)
tubesEventsOrig<-QUALIFIER:::.TubeNameMapping(db,tubesEvents=tubesEvents[,3,drop=F])
tubesEvents20090825<-QUALIFIER:::.TubeNameMapping(db,tubesEvents=tubesEvents[,2,drop=F])
tubesEvents20090622<-QUALIFIER:::.TubeNameMapping(db,tubesEvents=tubesEvents[,1,drop=F])
###80% of the pre-defined the value for each pannel
qaCheck(qaTask.list[["NumberOfEvents"]]
,formula=count ~ RecdDt | Tube
,outlierfunc=list(func=outlier.cutoff,args=list(lBound=0.8*tubesEvents20090825))
,subset=as.Date(RecdDt,"%m/%d/%y")>='2009-08-25'
)
qaCheck(qaTask.list[["NumberOfEvents"]]
,formula=count ~ RecdDt | Tube
,outlierfunc=list(func=outlier.cutoff,args=list(lBound=0.8*tubesEvents20090622))
,subset=as.Date(RecdDt,"%m/%d/%y")<'2009-08-25'&as.Date(RecdDt,"%m/%d/%y")>='2009-06-22'
)
qaCheck(qaTask.list[["NumberOfEvents"]]
,formula=count ~ RecdDt | Tube
,outlierfunc=list(func=outlier.cutoff,args=list(lBound=0.8*tubesEventsOrig))
,subset=as.Date(RecdDt,"%m/%d/%y")<'2009-06-22'
)
CairoX11()
plot(qaTask.list[["NumberOfEvents"]]
# ,count ~ RecdDt
,subset=Tube=='CD8/CD25/CD4/CD3/CD62L'
#,dest="image"
# ,scales=list(x=list(rot=45
# ,cex=0.5
# ))
# ,pch=19
)
#qaTask.list[["NumberOfEvents"]]@formula<-count ~ `RecdDt` | `t/Tube`:`t/PTID`
plot(qaTask.list[["NumberOfEvents"]]
# ,subset=id=='245'
# ,scatterPlot=TRUE
# ,scatterPar=list(stat=T)
)
clearCheck(qaTask.list[["NumberOfEvents"]])
##add new aggregated stats
QUALIFIER:::.addStats(qaTask.list[["BoundaryEvents"]]
,definition=sum(proportion)~RecdDt|fileid+gsid
,pop="/root/MNC/margin"
,statName="sum.prop"
)
head(subset(
queryStats(qaTask.list[["BoundaryEvents"]]
,y=sum.prop ~ RecdDt
,pop="margin"
# ,subset=value>0&id==806
)
,outlier==TRUE)
)
#check on the new stats
qaCheck(qaTask.list[["BoundaryEvents"]]
,sum.prop ~ RecdDt
,outlierfunc= list(func = outlier.cutoff,args=list(uBound=0.0003))
)
plot(qaTask.list[["BoundaryEvents"]]
,sum.prop ~ RecdDt
# ,subset=channel=="PE-A"
# &id==806
# ,ylab="sum(percent)"
# ,scatterPlot=T
# ,scatterPar=list(
# xlog=T
# ,stat=T
# )
,scales=list(format="%m/%d/%y")
# ,plotAll="none"
# ,dest="image"
)
#plot(qaTask.list[["BoundaryEvents"]]
# ,proportion ~ RecdDt|channel
## ,subset=channel=="PE-A"
## &id==806
# ,ylab="percent"
## ,scatterPlot=T
## ,scatterPar=list(
## xlog=T
## ,stat=T
## )
# ,scales=list(format="%m/%d/%y")
### ,plotAll=F
## ,dest="image"
#)
clearCheck(qaTask.list[["BoundaryEvents"]])
qaCheck(qaTask.list[["MFIOverTime"]]
# ,outlierfunc=outlier.norm
,rFunc=rlm
# ,Subset=channel%in%c('PE-Cy7-A')
# ,z.cutoff=10
)
head(subset(
queryStats(qaTask.list[["MFIOverTime"]]
# ,y=sum.prop ~ RecdDt
,pop="MFI"
# ,subset=value>0&id==806
)
,outlier==TRUE)
)
plot(qaTask.list[["MFIOverTime"]]
# ,y=MFI~RecdDt|stain
,subset=channel%in%c('APC-A')
&stain=="CD62L APC-A"
## &id==806
# ,rFunc=rlm
# ,scales=list(format="%m/%d/%y")
## ,scatterPlot=TRUE
# ,scatterPar=list(xlog=F)
# ,dest="image"
)
clearCheck(qaTask.list[["MFIOverTime"]])
qaCheck(qaTask.list[["RBCLysis"]]
,outlierfunc=list(func=outlier.cutoff
,args=list(lBound=0.9))
)
subset(
queryStats(qaTask.list[["RBCLysis"]]
,subset=Tube=='CD8/CD25/CD4/CD3/CD62L')
,outlier==TRUE)
plot(qaTask.list[["RBCLysis"]]
# ,subset=Tube=='CD8/CD25/CD4/CD3/CD62L'
# &id%in%c(270)
# , RecdDt~proportion | Tube
# ,scales=list(format="%m/%d/%y")
# ,ylab="percent"
# ,scatterPlot=T
# ,scatterPar=list(stat=T
# ,xbin=128)
# ,horiz=T
# ,dest="image"
# ,highlight="coresampleid"
# ,plotAll="none"
# ,width=27,height=13
)
clearCheck(qaTask.list[["RBCLysis"]])
qaCheck(qaTask.list[["spike"]]
,outlierfunc = list(func = outlier.t
,args = list(alpha=0.001
,isLower=FALSE)
)
)
plot(qaTask.list[["spike"]]
,y=spike~RecdDt|channel
,subset=Tube=='CD11c/CD80/DUMP/HLADr/CD123'
# ,dest="image"
# ,plotAll=T
)
plot(qaTask.list[["spike"]],y=spike~RecdDt|channel
,subset=channel=='FITC-A'
# &id%in%c(245,119)
# ,scatterPlot=TRUE
,scatterPar=list(ylog=T
,xlim=c(0,100)
# ,xbin=128
)
# ,dest="image"
# ,plotAll="none"
)
qaCheck(qaTask.list[["MNC"]]
# ,Subset=coresampleid%in%c(11730,8780)
# ,z.cutoff=0.1
)
plot(qaTask.list[["MNC"]]
,proportion~`coresampleid`
# , factor(coresampleid)~proportion
# ,par=list(horiz=TRUE)
)
#scatter plot for a sample group
plot(qaTask.list[["MNC"]]
,proportion~factor(coresampleid)
# ,par=list(xlab="coresampleid")
# , coresampleid ~proportion
# ,par=list(horiz=TRUE)
# ,subset=coresampleid%in%c(
## 11730
# 8780
# )
# ,scatterPlot=TRUE
,scatterPar=list(xbin=128
,stat=T)
,dest="~/rglab/workspace/QUALIFIER/output/image"
,plotAll=F
)
#scatter for one sample
plot(qaTask.list[["MNC"]]
,scatterPlot=TRUE
,subset=coresampleid==11730&id==245)
clearCheck(qaTask.list[["MNC"]])
qaCheck(qaTask.list[["RedundantStain"]]
# ,gOutlierfunc=qoutlier
# ,outlierfunc=qoutlier
# ,alpha=1.5
# ,z.cutoff=2
)
##example of passing lattice arguments
plot(qaTask.list[["RedundantStain"]]
,subset=channel=='APC-A'
# &stain%in%c('CD123','CD3')
# &coresampleid==11730
,y=proportion~factor(coresampleid)|channel:stain
# ,scatterPlot=T
,scatterPar=list(xlog=F
,stat=T
)
,scales=list(x=list(relation="free"))
# ,layout=c(2,NA,1)
# ,dest="image"
)
################################################################################
#4.qa report in html format
#set plotAll=TRUE to generate the scatter plots for all the individual FCS files
#otherwise only plots for outliers are generated.
###############################################################################
##customerize some of the task before pass them to report method
htmlReport(qaTask.list[["MFIOverTime"]])<-TRUE
rFunc(qaTask.list[["MFIOverTime"]])<-rlm
highlight(qaTask.list[["BoundaryEvents"]])<-"coresampleid"
#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")))
#modify functions within package namespace
funcToinsert <- ".postProcessSVG"
funcSym <- as.symbol(funcToinsert)
eval(substitute(environment(ff) <- getNamespace("QUALIFIER"), list(ff = funcSym)))
assignInNamespace(funcToinsert, eval(funcSym), ns = "QUALIFIER")
db <- load_db(path = "/home/wjiang2/rglab/workspace/QUALIFIER/output/preprocessedData")
qaTask.list <- db$qaTaskList
db$stats[sid == 3, value:= 0.1]
qaCheck(qaTask.list[["MNC"]]
, gOutlierfunc=list(func=outlier.norm
,args=list(alpha=0.1))
)
plot(qaTask.list[["MNC"]]
# , dest = "rglab/workspace/QUALIFIER/output/image"
# , plotAll = "none"
# , scatterPlot = T
# , subset = participantid == "002005"
# , scatterPar = list(xbin = 32)
)
qaReport(qaTask.list, outDir = "rglab/workspace/QUALIFIER/output/"
, plotAll = T
, subset = participantid == "002005"
)
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We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.