How to check the frequencies of gene mutations in TCGA cancer database [R]

[@VipinSharma-rr9gx]

Glad to see this Tutorial and Thank you for uploading😊

[@hanifullah1088]

Wonderful video with clear explanation

[@debajyotikabiraj4241]

Dear Madam, This is a very good tutorial video indeed. I would like to request that can you please furnish some good articles which reported such kind of study. Thank you

[@SouravMitra1991]

Great video! Keep up the good work.

[@Katchmagyk]

Great video! Thank you for making this

[@aidafall9152]

hey thank you for the video, so i have a question , can we use for an intron as intron 7 of betafibrinogene. will appreciate your reply

[@divyaagrawal6740]

GDCquery_Maf is removed from the latest version of the GDC

[@reflections86]

Hi. Thanks for the video. How I can use maftools to visualize genes mutated in a specific pathway from TCGA. Will appreciate your reply.

[@LiquidBrain]

Hi Imran, you may use the function "PlotOncogenicPathways" in maftools package. For example, if you want to visualise the mutated genes in RTK-RAS pathway: PlotOncogenicPathways(maf = laml, pathways = "RTK-RAS") -Lindsey

[@mehdihjamadi3225]

Hi thanks for the video. Is the mutation analysis via DNA sequencing or RNA sequencing?

[@LiquidBrain]

Hi I used Illumina RNAseq data for this mutation analysis. -Lind

[@mehdihjamadi3225]

@@LiquidBrain thanks for responding.

[@klaudia9159]

Hi, I have a question about this function maf_mutect2 % subset(Sequencer == "Illumina HiSeq 2000") %>% read.maf it dosen't work , why?

[@LiquidBrain]

Hi Klaudia, it seems that something has changed at the back end of the database and the code structure; I suggest you to seek explanation from the creators directly in the bioconductor forum. - Lindsey

[@juliangrandvallet5359]

Are they all hg19? or are there hg38 cohorts?

[@PeihuiBrandonYeo]

Great video

[@larshilgers54]

Hey great video! You restricted your data to include only data from one type of sequencer (Illumina HiSeq 2000). Should that always be done or is it fine to include all data regardless of sequencer used? Thanks!

[@LiquidBrain]

Hi Lars, glad you like it! Ya I don’t see why not as long as the downstream is just to visualise the discrete data (e.g. mutation status).

[@ssmunde6657]

Ma'am you might have checked mutation changes for stomach cancer. Are there chances to get mutation changes?

[@LiquidBrain]

Hi there, unfortunately I didn’t check for stomach cancer, you may check it by running the R script that I linked above and I believe the abbreviation for stomach cancer is “TCGA-STAD”

[@mukund2684]

Hi, great video! I am getting an error: could not find function "GDCquery_Maf" while executing the following command: maf_mutect2 % subset(Sequencer == "Illumina HiSeq 2000") %>% read.maf I would appreciate if you could help me with this.

[@LiquidBrain]

Hi there, tcgabiolinks has recently did some modification on their scripts, perhaps you could raise up the question in their platform github.com/BioinformaticsFMRP/TCGAbiolinks/issues -Lindsey

[@aleddak3848]

TCGAbiolinks removed this function since the TCGA updates, please use GDCquery instead

[@mahsaehsanifard9548]

good. tnx