From f40a068a3551df8ace8885ba1eb999af061d96ff Mon Sep 17 00:00:00 2001
From: tiagochst <tiagochst@gmail.com>
Date: Sun, 13 Nov 2016 20:00:03 -0200
Subject: [PATCH] Finishing to clean functions with old TCGAquery_clinic

---
 R/TCGAanalyze.R               |  4 +---
 R/TCGAquery_clinical.R        | 18 ------------------
 man/TCGAanalyze_SurvivalKM.Rd |  4 +---
 man/TCGAquery_clinicFilt.Rd   |  3 +--
 4 files changed, 3 insertions(+), 26 deletions(-)

diff --git a/R/TCGAanalyze.R b/R/TCGAanalyze.R
index 62bbda9f0..12a7c1602 100644
--- a/R/TCGAanalyze.R
+++ b/R/TCGAanalyze.R
@@ -168,14 +168,12 @@ TCGAanalyze_Preprocessing <- function(object,
 #' @export
 #' @return table with survival genes pvalues from KM.
 #' @examples
-#' \dontrun{
-#'  clinical_patient_Cancer <- TCGAquery_clinic("brca","clinical_patient")
+#'  clinical_patient_Cancer <- GDCquery_clinic("TCGA-BRCA","clinical")
 #'  dataBRCAcomplete <- log2(BRCA_rnaseqv2)
 #'  # Selecting only 10 genes for example
 #'  dataBRCAcomplete <- dataBRCAcomplete[1:10,]
 #'  tabSurvKM<-TCGAanalyze_SurvivalKM(clinical_patient_Cancer,dataBRCAcomplete,
 #'  Genelist = rownames(dataBRCAcomplete), Survresult = FALSE,ThreshTop=0.67,ThreshDown=0.33)
-#' }
 TCGAanalyze_SurvivalKM<-function(clinical_patient,dataGE,Genelist, Survresult,
                                  ThreshTop=0.67, ThreshDown=0.33,p.cut=0.05){
 
diff --git a/R/TCGAquery_clinical.R b/R/TCGAquery_clinical.R
index fb9945855..d72b34097 100644
--- a/R/TCGAquery_clinical.R
+++ b/R/TCGAquery_clinical.R
@@ -516,23 +516,6 @@ parseXML <- function(files, xpath, clinical.info ){
     return(clin)
 }
 
-update.clinical.with.last.followup <- function(clin){
-
-    for(disease in unique(clin$disease)){
-        aux <- clinical.table[,disease]
-        files <- rownames(clinical.table[which(aux==1),])
-        # get last follow up files not nte
-        files <- sort(files[grepl("follow",files) & !grepl("nte",files)],decreasing = T)[1]
-
-        follow <- TCGAquery_clinic(disease,files)
-
-        colnames(follow) [colnames(follow) %in% colnames(clin)]
-        aux <- plyr::ddply(follow, .(bcr_patient_barcode), function(x) x[c(nrow(x)), ])
-        aux <- aux[aux$bcr_patient_barcode %in% clin$bcr_patient_barcode,colnames(aux) %in% colnames(clin)]
-        clin[na.omit(match(aux$bcr_patient_barcode,clin$bcr_patient_barcode)),match(colnames(aux),colnames(clin))] <- aux
-    }
-    return(clin)
-}
 
 #' @title Filter samples using clinical data
 #' @description
@@ -540,7 +523,6 @@ update.clinical.with.last.followup <- function(clin){
 #'   Filters available: HER, ER,gender,PR, stage.
 #' @param barcode List of barcodes
 #' @param clinical_patient_data clinical_patient_data obtained with clinic function
-#' Ex: clinical_patient_data <- TCGAquery_clinic("LGG","clinical_patient")
 #' @param HER  her2 neu immunohistochemistry receptor status: "Positive" or "Negative"
 #' @param gender "MALE" or "FEMALE"
 #' @param PR  Progesterone receptor status: "Positive" or "Negative"
diff --git a/man/TCGAanalyze_SurvivalKM.Rd b/man/TCGAanalyze_SurvivalKM.Rd
index b64c67a28..821e2289b 100644
--- a/man/TCGAanalyze_SurvivalKM.Rd
+++ b/man/TCGAanalyze_SurvivalKM.Rd
@@ -45,13 +45,11 @@ from survival package
 }
 }
 \examples{
-\dontrun{
- clinical_patient_Cancer <- TCGAquery_clinic("brca","clinical_patient")
+ clinical_patient_Cancer <- GDCquery_clinic("TCGA-BRCA","clinical")
  dataBRCAcomplete <- log2(BRCA_rnaseqv2)
  # Selecting only 10 genes for example
  dataBRCAcomplete <- dataBRCAcomplete[1:10,]
  tabSurvKM<-TCGAanalyze_SurvivalKM(clinical_patient_Cancer,dataBRCAcomplete,
  Genelist = rownames(dataBRCAcomplete), Survresult = FALSE,ThreshTop=0.67,ThreshDown=0.33)
 }
-}
 
diff --git a/man/TCGAquery_clinicFilt.Rd b/man/TCGAquery_clinicFilt.Rd
index fe59374c8..a5f4f4bc5 100644
--- a/man/TCGAquery_clinicFilt.Rd
+++ b/man/TCGAquery_clinicFilt.Rd
@@ -10,8 +10,7 @@ TCGAquery_clinicFilt(barcode, clinical_patient_data, HER = NULL, ER = NULL,
 \arguments{
 \item{barcode}{List of barcodes}
 
-\item{clinical_patient_data}{clinical_patient_data obtained with clinic function
-Ex: clinical_patient_data <- TCGAquery_clinic("LGG","clinical_patient")}
+\item{clinical_patient_data}{clinical_patient_data obtained with clinic function}
 
 \item{HER}{her2 neu immunohistochemistry receptor status: "Positive" or "Negative"}