R/MMRFclinical.R

In MarzyUnicz/MMRFBiolinks:

#' @title Get GDC clinical data
#' @description
#' MMRFqueryGDC_clinic will download and prepare all clinical information from the API
#' as the one with using the button from each project
#' @param type A valid type. Options "clinical", "Biospecimen"  (see list with getGDCprojects()$project_id)]
#' @param save.csv Write clinical information into a csv document
#' @export
#' @importFrom data.table rbindlist as.data.table
#' @importFrom jsonlite fromJSON
#' @importFrom TCGAbiolinks GDCquery_clinic
#' @examples
#' clin.mm<-MMRFqueryGDC_clinic(type = "clinical")
#' clin.mm<-MMRFqueryGDC_clinic(type = "biospecimen")
#' @return A data frame with the clinical information




MMRFqueryGDC_clinic<- function(type = "clinical", save.csv = FALSE){
  
  clin<-GDCquery_clinic(project="MMRF-COMMPASS", type, save.csv)
  
  #names(clin)[names(clin) == 'submitter_id'] <- 'bcr_patient_barcode'
  
  #if clinical
  
  if (type!="clinical" & type!="Biospecimen" ){
    return("Error message: type does not exist")
  }
  
  if (type=="clinical"){
    names(clin)[1] <- "bcr_patient_barcode"
    
  }
  else if  (type=="Biospecimen"){
    bcr_patient_barcode.sub<-clin[colnames(clin)=='submitter_id']
    colnames(bcr_patient_barcode.sub)[1]<-"bcr_patient_barcode"
    bcr_patient_barcode.sub$bcr_patient_barcode<-substr(bcr_patient_barcode.sub$bcr_patient_barcode,1,9)
    clin<-cbind(bcr_patient_barcode.sub,clin)
    
  }
  
  
  return(clin)
  
}






#' @title Get list of treatments 
#' @description
#' get all treatmentsSearch patient clinical information filtered by therapy name
#' @param clin.mm is a data.frame using function 'clinic' with information
#' related to barcode / samples such as bcr_patient_barcode, days_to_death ,
#' days_to_last_follow_up , vital_status, etc
#' @export
#' @return a data.frame 




MMRFgetGDC_Treatments<- function(clin.mm){ 
  
  df<-NULL
  
  treat.list<-clin.mm$treatments
  for(i in 1:length(treat.list)){
    treat.aux<-as.data.frame(treat.list[[i]])
    barcode<-substring(treat.aux$submitter_id,1,9)
    treat<-treat.aux$therapeutic_agents
    line<-treat.aux$regimen_or_line_of_therapy
    df<-rbind(df, data.frame(barcode,treat,line))
    
  }  
  
  
  return(unique(df))
}





#' @title Get Search patient clinical information filtered by therapy name
#' @description
#' Search patient clinical information filtered by therapy name
#' @param therapyname Therapy name
#' @param clin.mm is a data.frame using function 'clinic' with information
#' related to barcode / samples such as bcr_patient_barcode, days_to_death ,
#' days_to_last_follow_up , vital_status, etc
#' @export
#' @return a character vector with the barcodes




MMRFgetGDC_BarcodeTherapy<- function(therapyname,clin.mm){  
  
  treat.tab<-MMRFgetGDC_Treatments(clin.mm)
  barcode<-NULL
  
  for (i in 1:length(therapyname)) {
    df<-filter(treat.tab,treat==therapyname[i])
    barcode<-union(barcode,df$barcode)
  }
  
  return(unique(barcode))
}




  




  
#' @title Get Best Overall response 
#' @description
#' Search patient clinical information filtered by therapy name
#' @param barcode is a vector of patient barcode
#' @param trt.resp is a data.frame of clinical information downloaded from MMRF-Commpass Researcher Gateway 
#' and imported into environment
#' @export
#' @return a character vector with the barcodes




MMRFgetGateway_BestOverallResponse<- function(barcode,treat.resp){ 
  inter<-intersect(barcode,treat.resp$public_id)  
  
  filt<-treat.resp[treat.resp$public_id %in% inter,]
  filt<-filt[,c("public_id","trtname","trtshnm","bestresp","bestrespsh")] 
  
  
  
  return(filt)
}