An R Package for computing Guan Rank • GuanRankR

Overview

An R Package for computing Guan Rank, which transforms survival data in to an easy to model ranking

The method was used in many of Prof. Yuanfang Guan’s top performing DREAM Challenge models

Installation

Install the released version of GuanRankR from Github:

remotes::install_github(repo = "Systems-Methods/GuanRankR")

Or:

remotes::install_git(
  'https://github.com/Systems-Methods/GuanRankR.git'
)

Or install the development version

remotes::install_github(repo = "Systems-Methods/GuanRankR", 
                        ref = "develop")

Example

Example Data

First we can use the {UCSCXenaTools} package to download an example mRNASeq dataset.

dat <- UCSCXenaTools::getTCGAdata(project = "LUAD", 
                                  clinical = TRUE, 
                                  download = TRUE,
                                  quiet = TRUE)
#> This will check url status, please be patient.
#> All downloaded files will under directory /var/folders/f8/kyzn816j4pn7wwt6kb95xg1w0000gn/T//Rtmp8mPBUY.
#> The 'trans_slash' option is FALSE, keep same directory structure as Xena.
#> Creating directories for datasets...
#> Downloading TCGA.LUAD.sampleMap/LUAD_clinicalMatrix

clin <- data.table::fread(dat$destfiles, data.table = FALSE)

Create Survival Data and Run Ranks


survData <- data.frame(
  time = ifelse(!is.na(clin$days_to_last_followup),
                as.numeric(clin$days_to_last_followup),
                as.numeric(clin$days_to_death)),
  status = dplyr::recode(
    clin$vital_status, 'LIVING' = 0,'DECEASED' = 1, .default = NA_real_
  )
)

gr <- GuanRankR::calculate_guan_rank(surv_data = survData)

Plotting Results

Col <- as.vector(factor(gr$status, labels = c('slategrey', 'cyan')))
par(mfrow = c(2,2))
plot(survival::survfit(survival::Surv(gr$time, gr$status)~1), xlab = "Days",
     ylab = "Survival %", conf.int = FALSE, mark.time = TRUE, col = "slategrey",
     cex = .5, main = 'LUAD')
plot(gr$time,gr$guan_rank, pch = 19, col = Col, cex = .5, xlab = "Days",
     ylab = "Guan Rank", main = "Guan Rank vs Time")
boxplot(gr$guan_rank ~ gr$status, xlab = "Status", ylab = "Guan Rank",
        main = "Guan Rank vs Status")
hist(gr$guan_rank, breaks = 30, xlab = "Guan Rank",
     main = "Guan Rank Distribution")

Code of Conduct

Please note that the GuanRankR project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.