Troubleshooting

Adding additional covariates to the analysis dataframe

What if you have already preprocessed the data, but you want to add additional covariates to the phenotype dataframe for your analysis? See below:

## Creating new variable from existing data columns 

phenodataframe<-as.data.frame(pData(processedOut$mset))
phenodataframe$LBWbin<-ifelse(phenodataframe$BWT<2500,1,0)
phenodataframe$HBWbin<-ifelse(phenodataframe$BWT>4000,1,0)

## adding more data to the dataframe
## assuming there is a common identifer across the two datasets

morecovariates<-read.csv("additionalcovariates.csv")
phenodataframe<-merge(phenodataframe,morecovariates,by="SampleID")
rownames(phenodataframe)<-as.character(phenodataframe$Basename) ## just making sure the rownames are the Basename

## then just run the analysis with the dataset 
## the dataAnalysis function will make sure the Basenames are in the same order 
## for the beta-value matrix and the phenotype dataframe

tempresults<-dataAnalysis(phenofinal=phenodataframe,
                          betafinal=processedOut$processedBetas,
                          array="450K",
                          maxit=100,
                          Omega=processedOut$Omega,
                          vartype="OutcomeCont",
                          varofinterest="Gestage",
                          Table1vars=c("BWT","Sex","Age","Parity","MaternalEd",
                                       "Smoke","preBMI","ModeDelivery","Ethnic"),
                          StratifyTable1=FALSE,
                          StratifyTable1var=NULL,
                          adjustmentvariables=c("BWT","Sex","Age","Parity","MaternalEd",
                                                "Smoke","preBMI","ModeDelivery","Ethnic"),
                          RunUnadjusted=TRUE,
                          RunAdjusted=TRUE,
                          RunCellTypeAdjusted=TRUE,
                          RunSexSpecific=TRUE,
                          RestrictToSubset=TRUE,
                          RestrictionVar="NoPregnancyComplications",
                          RestrictToIndicator="Yes",
                          destinationfolder="H:\\UCLA\\PACE\\Gestationalage-placenta",
                          savelog=TRUE,
                          cohort="HEBC",analysisdate="20210103",
                          analysisname="sensitivtyanalysis")

If you find you are no longer seeing results in your R console

Each of the PACEanalysis functions automatically create a log file to catch any warnings or errors encountered while running the function, which helps to troubleshoot any issues encountered. If the function fails to run completely (e.g. if it encounters an error), the log file will not be closed, and anything you run in R will be logged into that file instead of showing up in your R console. To close the open log file, run the below in your R console:

sink()
sink(type="message")

Different Errors

Error in dataAnalysis(phenofinal = temppheno, betafinal = processedOut$processedBetas : One of the adjustment variables is not in the dataset

This means that one of the adjustment variables you specified in the dataAnalysis function adjustmentvariables argument is not in the phenofinal data.frame. Check the column names in the data.frame you specified for the phenofinal argument, are the adjustment variables in there?

tempadjustmentvariables<-c("Sex","Age","Parity","MaternalEd",
                                   "Smoke","preBMI","ModeDelivery","Ethnic")
colnames(temppheno)

## let's check which of the specified adjustment variables are not in 
## the data.frame we specified for our phenofinal argument
tempadjustmentvariables[!(tempadjustmentvariables %in% colnames(temppheno))]

Error in setwd(destinationfolder) : cannot change working directory

The specified destination folder for the function does not exist, make sure you create that folder first

If you encounter a different error

Please send the log file from the function to Alexandra (ambinder@hawaii.edu); she developed and maintains the PACEanalysis package and can help troubleshoot the issue.