Plots all the pathological grades of the EMRs.This should only be run after all the BarrettsDataAccord functions.

BarrettsEMRGrades(EndoSubsetEMR)

Arguments

EndoSubsetEMR

The dataset.

Examples

# Firstly relevant columns are extrapolated from the # Mypath demo dataset. These functions are all part of Histology data # cleaning as part of the package. v<-HistolDx(Mypath,'Diagnosis') v<-HistolExtrapolDx(v,'Diagnosis')
#> Error in paste0("[Cc]arcin|[Cc]ance|[Ll]ymphoma|[Tt]umour|[Dd]yspla|G[Ii][Ss][Tt]|[Ss]tromal|[Ll]eio|[Cc]rohn", userString): argument "userString" is missing, with no default
v<-HistolNumbOfBx(v,'Macroscopicdescription','specimen') v<-HistolBxSize(v,'Macroscopicdescription') # The histology is then merged with the Endoscopy dataset. The merge occurs # according to date and Hospital number v<-Endomerge2(Myendo,'Dateofprocedure','HospitalNumber',v,'Dateofprocedure', 'HospitalNumber') #The function relies on the other Barrett's functions being run as well: b1<-Barretts_PragueScore(v,'Findings') b2<-Barretts_PathStage(b1,'Histology') b3<-Barretts_EventType(b2,'Histology', 'ProcedurePerformed','Indications','Findings') # The follow-up group depends on the histology and the Prague score for a # patient so it takes the processed Barrett's data and then looks in the # Findings column for permutations of the Prague score. b4<-Barretts_FUType(b3,'Findings') colnames(b4)[colnames(b4) == 'pHospitalNum'] <- 'HospitalNumber' # The function extracts only those rows for patients who have undergone # EMR and then extracts the EMR grade from the extracted worst histopath # column (called IMorNoIM). This is then plotted out. kk<-BarrettsEMRGrades(b4)
#> Error in plot.new(): figure margins too large
rm(v)