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: [email protected]
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