update.survival.from.followup: Update clinical data from follow-up table

In averissimo/glmSparseNetPaper:

Description

Survival and vital status are not updated in the clinical data obtained from TCGA, so we need to do it manually.

Usage

update.survival.from.followup(clinical, follow.up)

Arguments

clinical	data.frame with clinical information from TCGA project
follow.up	data.frame with follow-up information from TCGA project

Details

The data is assumed to be obtained from TCGAbiolinks

Examples

library(dplyr)
data(clinical, gdc, package = 'skcm.data')
clinical.new <- update.survival.from.followup(clinical$all, gdc$follow.up)

problem.barcodes <- c('TCGA-FR-A726', 'TCGA-D3-A8GP', 'TCGA-DA-A1HW', 'TCGA-DA-A1I1',
                      'TCGA-DA-A1I5', 'TCGA-DA-A1I7', 'TCGA-DA-A1IB', 'TCGA-DA-A95W',
                      'TCGA-DA-A95X', 'TCGA-EB-A41A', 'TCGA-EE-A2GJ', 'TCGA-FR-A726',
                      'TCGA-HR-A5NC', 'TCGA-XV-A9VZ')

clinical.new %>% filter(bcr_patient_barcode %in% problem.barcodes)


#
#
# Original clinical information from TCGAbiolinks

clinical$all %>% filter(bcr_patient_barcode %in% problem.barcodes) %>%
 select(bcr_patient_barcode, days_to_last_followup, days_to_death, vital_status,
        year_of_form_completion, month_of_form_completion, day_of_form_completion) %>% arrange(bcr_patient_barcode)

#
#
# Original follow-up information from TCGAbiolinks

gdc$follow.up %>% filter(bcr_patient_barcode %in% problem.barcodes) %>%
 select(bcr_patient_barcode, days_to_last_followup, days_to_death, vital_status,
        year_of_form_completion, month_of_form_completion, day_of_form_completion) %>% arrange(bcr_patient_barcode)

averissimo/glmSparseNetPaper documentation built on Jan. 25, 2021, 12:11 p.m.