Play all

Intro

Intuition behind survival analysis

Why do we perform survival analysis?

What is Censoring and why is it important?

What is considered as an event?

Methods for survival analysis

How to read a Kaplan-Meier curve?

Question to answer using survival analysis

3 things required for survival analysis

Download clinical data from GDC portal

Getting status information and censoring data

Set up an “overall survival” i.e. time for each patient in the cohort

For event/strata information for each patient, fetch gene expression data from GDC portal

Build query using GDCquery

Download data using GDCdownload

Extract counts using GDCprepare

Perform Variance Stabilization Transformation vst on counts before further analysis

Wrangle data to get the relevant data and data in the right shape

Approaches to divide cohort into 2 groups based on expression

Bifurcating patients into low and high TP53 expression groups

Define strata for each patient

Compute a survival curve using survfit and creating a Kaplan-Meier curve using ggsruvplot

survfit vs survdiff

Description:

Learn how to perform survival analysis using TCGA data in R, focusing on creating Kaplan-Meier curves. Explore the concept of survival analysis, its applications, and essential components like censoring. Discover methods for survival analysis and how to interpret Kaplan-Meier curves. Follow step-by-step instructions to download clinical data from the GDC portal, prepare gene expression data, and perform variance stabilization transformation. Master techniques for dividing cohorts based on expression levels, defining strata, and computing survival curves using survfit() and ggsruvplot(). Gain practical skills in utilizing the survival and survminer packages to conduct comprehensive survival analysis in R.

Survival Analysis with TCGA Data in R - Create Kaplan-Meier Curves

Bioinformagician

Add to list

#Mathematics #Statistics & Probability #Survival Analysis #Data Science #Bioinformatics #Data Analysis #Programming #Domain-Specific Languages (DSL) #R Programming #Science #Biology #Genomics

0:00 / 0:00