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PoisonAlien / maftools

Summarize, Analyze and Visualize MAF files from TCGA or in-house studies.
http://bioconductor.org/packages/release/bioc/html/maftools.html
MIT License
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an splice_region variant does not appear in the oncoplot #998

Closed FerTalavera closed 8 months ago

FerTalavera commented 9 months ago

Hi, I have a splice region variant (deletion) that does not appear in the oncoplot. I have tried with other variants of the same type, and the same occurs. I also already checked the MAF file, and the variants are there. Is this an issue with the package?

PoisonAlien commented 9 months ago

Hi,

It's hard to guess the problem. Could you please provide a reproducible example?

FerTalavera commented 9 months ago

Hi,

I've attached a maf that contains a splice region variant in Khsrp but it does not appear in the oncoplot as you can see in the image.

I'll appreciate your help.

Bw,

Fernanda Talavera

De: Anand Mayakonda @.> Enviado: jueves, 4 de enero de 2024 02:02 a. m. Para: PoisonAlien/maftools @.> Cc: MARIA FERNANDA TALAVERA CRUZ @.>; Author @.> Asunto: Re: [PoisonAlien/maftools] an splice_region variant does not appear in the oncoplot (Issue #998)

Hi,

It's hard to guess the problem. Could you please provide a reproducible example?

— Reply to this email directly, view it on GitHubhttps://github.com/PoisonAlien/maftools/issues/998#issuecomment-1876670644, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AVFP7SMBQIN7HPJQEAI3TK3YMZOZZAVCNFSM6AAAAABBHEJBO2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQNZWGY3TANRUGQ. You are receiving this because you authored the thread.Message ID: @.***>

PoisonAlien commented 9 months ago

Hi,

The attachment seems to be missing. Could you please try again?

FerTalavera commented 9 months ago

Sure, here I attached it again.

De: Anand Mayakonda @.> Enviado: viernes, 5 de enero de 2024 01:56 a. m. Para: PoisonAlien/maftools @.> Cc: MARIA FERNANDA TALAVERA CRUZ @.>; Author @.> Asunto: Re: [PoisonAlien/maftools] an splice_region variant does not appear in the oncoplot (Issue #998)

Hi,

The attachment seems to be missing. Could you please try again?

— Reply to this email directly, view it on GitHubhttps://github.com/PoisonAlien/maftools/issues/998#issuecomment-1878267733, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AVFP7SLF22BYU34OMYHNDP3YM6W23AVCNFSM6AAAAABBHEJBO2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQNZYGI3DONZTGM. You are receiving this because you authored the thread.Message ID: @.***>

PoisonAlien commented 8 months ago

Hi, Unfortunately, I still can not see the attachment.

FerTalavera commented 8 months ago

Hi, are you seeing these messages in your email inbox or on GitHub?

Get Outlook for iOShttps://aka.ms/o0ukef

From: Anand Mayakonda @.> Sent: Sunday, January 7, 2024 10:10:14 AM To: PoisonAlien/maftools @.> Cc: MARIA FERNANDA TALAVERA CRUZ @.>; Author @.> Subject: Re: [PoisonAlien/maftools] an splice_region variant does not appear in the oncoplot (Issue #998)

Hi, Unfortunately, I still can not see the attachment.

— Reply to this email directly, view it on GitHubhttps://github.com/PoisonAlien/maftools/issues/998#issuecomment-1880100711, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AVFP7SJ6CMJKP2YQ7VD6JXTYNLCGNAVCNFSM6AAAAABBHEJBO2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQOBQGEYDANZRGE. You are receiving this because you authored the thread.Message ID: @.***>

PoisonAlien commented 8 months ago

Hi,

I checked both. There is no attachement. You can email if you would like.

FerTalavera commented 8 months ago

Hi,

Thanks, I just sent it to your email, I hope you can see it now.

De: Anand Mayakonda @.> Enviado: domingo, 7 de enero de 2024 10:41 a. m. Para: PoisonAlien/maftools @.> Cc: MARIA FERNANDA TALAVERA CRUZ @.>; Author @.> Asunto: Re: [PoisonAlien/maftools] an splice_region variant does not appear in the oncoplot (Issue #998)

Hi,

I checked both. There is no attachement. You can @.***> if you would like.

— Reply to this email directly, view it on GitHubhttps://github.com/PoisonAlien/maftools/issues/998#issuecomment-1880108619, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AVFP7SPKB3CW7D476CRTKRLYNLF5HAVCNFSM6AAAAABBHEJBO2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQOBQGEYDQNRRHE. You are receiving this because you authored the thread.Message ID: @.***>

PoisonAlien commented 8 months ago

Thanks. I received the file. I will get back to you soon.

FerTalavera commented 8 months ago

Ok :) thanks!

Get Outlook for iOShttps://aka.ms/o0ukef

From: Anand Mayakonda @.> Sent: Sunday, January 7, 2024 11:04:50 AM To: PoisonAlien/maftools @.> Cc: MARIA FERNANDA TALAVERA CRUZ @.>; Author @.> Subject: Re: [PoisonAlien/maftools] an splice_region variant does not appear in the oncoplot (Issue #998)

Thanks. I received the file. I will get back to you soon.

— Reply to this email directly, view it on GitHubhttps://github.com/PoisonAlien/maftools/issues/998#issuecomment-1880113983, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AVFP7SMZOH7YBWPHTUVEBKLYNLITFAVCNFSM6AAAAABBHEJBO2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQOBQGEYTGOJYGM. You are receiving this because you authored the thread.Message ID: @.***>

PoisonAlien commented 8 months ago

Hi, Thanks for the file again. Splice_Region variants are considered silent since they are of LOW functional impact. If you would still like to include them, you can just define your variant classifications to be considered nonsynonymous while importing the MAF file.

vc.nonSilent = c("Frame_Shift_Del", "Frame_Shift_Ins", "Splice_Site", "Translation_Start_Site",
                     "Nonsense_Mutation", "Nonstop_Mutation", "In_Frame_Del",
                     "In_Frame_Ins", "Missense_Mutation", "Splice_Region")

m = maftools::read.maf(maf = "~/Downloads/all_mafs_merged.maf", vc_nonSyn = vc.nonSilent)

I hope this helps.

P.S: Mouse genomes are not fully supported in maftools. Please be careful with some analyses.

FerTalavera commented 8 months ago

Oh, ok, I'll try that. Thank you so much for your help and the heads-up regarding mouse genome compatibility. :)

De: Anand Mayakonda @.> Enviado: domingo, 7 de enero de 2024 12:07 p. m. Para: PoisonAlien/maftools @.> Cc: MARIA FERNANDA TALAVERA CRUZ @.>; Author @.> Asunto: Re: [PoisonAlien/maftools] an splice_region variant does not appear in the oncoplot (Issue #998)

Hi, Thanks for the file again. Splice_Region variants are considered silent since they are of LOW functional impacthttp://www.ensembl.org/info/genome/variation/prediction/predicted_data.html. If you would still like to include them, you can just define your variant classifications to be considered nonsynonymous while importing the MAF file.

´´´r vc.nonSilent = c("Frame_Shift_Del", "Frame_Shift_Ins", "Splice_Site", "Translation_Start_Site", "Nonsense_Mutation", "Nonstop_Mutation", "In_Frame_Del", "In_Frame_Ins", "Missense_Mutation", "Splice_Region")

m = maftools::read.maf(maf = "~/Downloads/all_mafs_merged.maf", vc_nonSyn = vc.nonSilent) ´´´

I hope this helps.

P.S: Mouse genomes are not fully supported in maftools. Please be careful with some analyses.

— Reply to this email directly, view it on GitHubhttps://github.com/PoisonAlien/maftools/issues/998#issuecomment-1880129273, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AVFP7SMDLEF33XSJKINBEK3YNLP53AVCNFSM6AAAAABBHEJBO2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQOBQGEZDSMRXGM. You are receiving this because you authored the thread.Message ID: @.***>