@@ -1,7 +1,7 @@

 Package: TCGAbiolinks

 Type: Package

 Title: TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data

-Version: 2.35.3

+Version: 2.35.4

 Date: 2024-01-01

 Author: Antonio Colaprico,

     Tiago Chedraoui Silva,

@@ -229,7 +229,7 @@ GDCquery_clinic <- function(

     options.pretty <- "pretty=true"

     if (grepl("clinical",type,ignore.case = TRUE)) {

-        options.expand <- "expand=diagnoses,diagnoses.treatments,annotations,family_histories,demographic,exposures"

+        options.expand <- "expand=diagnoses,follow_ups,diagnoses.treatments,annotations,family_histories,demographic,exposures"

         option.size <- paste0("size=",getNbCases(project,"Clinical"))

         files.data_category <- "Clinical"

     } else {

@@ -266,7 +266,7 @@ GDCquery_clinic <- function(

     #message(paste0(baseURL,paste(options.pretty,options.expand, option.size, options.filter, sep = "&")))

     results <- json$data$hits

-

+    saveRDS(results,"tcgabiolinks_debug.rda")

     if (grepl("clinical",type,ignore.case = TRUE)) {

         if (grepl("TCGA",project)) {

             df <- data.frame("submitter_id" = results$submitter_id)

@@ -276,6 +276,7 @@ GDCquery_clinic <- function(

                 # we are getting more results than what we should

                 diagnoses <- diagnoses[diagnoses$submitter_id %in% df$submitter_id,]

+                diagnoses$days_to_last_follow_up <- NULL

                 df <- merge(df,diagnoses, by="submitter_id", all = TRUE, sort = FALSE)

             }

@@ -300,6 +301,23 @@ GDCquery_clinic <- function(

                 )

             }

+            if ("follow_ups" %in% colnames(results)){

+                follow_ups <- rbindlist(lapply(results$follow_ups, function(x) if(is.null(x)) data.frame(NA) else x),fill = T)

+                follow_ups$submitter_id <- gsub("_follow_up*","", follow_ups$submitter_id)

+

+                # we are getting more results than what we should

+                follow_ups <- follow_ups[follow_ups$submitter_id %in% df$submitter_id,]

+

+                # Get the max value of days to follow up

+                follow_ups_last <- follow_ups %>%

+                    dplyr::group_by(submitter_id) %>%

+                    dplyr::summarise(

+                        days_to_last_follow_up = ifelse(any(!is.na(days_to_follow_up)),max(days_to_follow_up,na.rm = TRUE),NA)

+                    )

+

+                df <- dplyr::full_join(df,follow_ups_last, by = "submitter_id")

+            }

+

             if( "treatments" %in% colnames(df)) {

                 treatments <- purrr::map_dfr(