continues to remove redundant functions

DESCRIPTION

@@ -1,20 +1,19 @@
 Package: brca.data.2018.09.13
 Title: Gene expression and clinical data from Breast invasive carcinoma from TCGA.
-Version: 1.0
+Version: 1.1
 Authors@R: person("André", "Veríssimo", email = "[email protected]", role = c("aut", "cre"))
 Description: Contains the datasets for BRCA (Breast) with gene expression, mutation
              and clinical data. All was extracted from TCGA.
              Data was downloaded in 2018.09.13 and processed using build_data.Rmd vignette
-Depends:
-    R (>= 3.3.2)
+Depends: R (>= 3.3.2),
+    tcga.data.utils
 License: GPL-3
 Imports: Biobase,
     SingleCellExperiment,
     MultiAssayExperiment,
     dplyr,
     futile.logger,
-    TCGAutils,
-    tcga.data.utils
+    TCGAutils
 Encoding: UTF-8
 LazyData: true
 Suggests: TCGAbiolinks,

NAMESPACE

@@ -1,7 +1,2 @@
 # Generated by roxygen2: do not edit by hand
 
-export(update.survival.from.followup)
-export(build.assay)
-export(build.matrix)
-export(getParticipantCode)
-importFrom(dplyr,"%>%")

vignettes/build_data.Rmd

@@ -250,7 +250,7 @@ follow.up              <- gdc$follow.up
 levels(clinical$vital_status) <- levels(clinical$vital_status) %>% {replace(., . == '', NA)}
 levels(follow.up$vital_status)    <- levels(follow.up$vital_status) %>% {replace(., . == '', NA)}
 
-updated.surv           <- update.survival.from.followup(clinical, follow.up) %>% as.data.frame
+updated.surv           <- updateSurvivalFromFollowup(clinical, follow.up) %>% as.data.frame
 rownames(updated.surv) <- updated.surv$bcr_patient_barcode
 
 clinical$surv_event_time <- updated.surv[clinical$bcr_patient_barcode, 'surv_event_time']