In lootpiz/PatiDem: Characterization of PATIent DEMographics

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

Introduction

A package to characterize patient demographics

Install the package

intall.packages("devtools")
library(devtools)
devtools::install_github("lootpiz/PatiDem")

Load the package

library(PatiDem)

Download the TCGA metadata

tcga <- downloadData()

Generate a boxplot

visualizationBox(tcga, cancer_type = c("BLCA", "BRCA"),
    phenotype = "age_at_initial_pathologic_diagnosis",
    metadata_col = "race",
    metadata_levels = c("WHITE", "ASIAN"))

Statistical testing

df <- data.frame(column_one = tcga$gender, column_two = tcga$vital_status)
statisticalTesting(df, categorical = T)

df <- data.frame(column_one = tcga$age, column_two = tcga$race)
statisticalTesting(df, categorical = F)