Cancer Somatic Mutation Analysis | MAFtools R Package

Many cancer are a direct results of somatic mutation (not from the germline) due to their instable chromosome. This could be direct outcome of a faulty repair system, or other environment factors. Thus, is it often useful to understand the type of mutation in the cancer and how much such mutation have impact the survivability and the severity of the patient. Maftools was developed with this in mine, using the original Mutation annotation format (MAF), this tools provide a large number of ways for the user to understand the type of mutation in each cancer group and how are the mutation as compared to the other. Original script file https://github.com/PoisonAlien/maftools Script for video https://github.com/brandonyph/LiquidB... Email: liquidbrain.r@gmail.com Website: https://www.liquidbrain.org/videos Patreon:   / liquidbrain   Chapters 0:00 Intro 1:10 intro to R 2:35 Installation of Package 4:04 Importing MAF manually 5:52 Importing from TCGA 8.04 Sub setting MAF 9:14 Merging MAF 10:31 Plot maf summary() 12:11 Oncoplot() 13:30 Transition and Transversion plot() 14:45 Lollipop 16:20 Rainfall plot 18:19 Comparing mutation to other TCGA 19:15 Plotting VAF 21:02 Copy number variation 23:30 Oncoplot (Copy number variation) 24:10 Circular binary segmentation 25:10 Somatic interaction 26:44 Detecting Cancer Driver 28:25 detecting pfam domain 28:59 Survival Analysis 30.07 Detecting survival trend 31:48 Comparing two cancer cohort 32:49 Forest plot 35:13 Clinical data analysis