read.maf

[Naziaahmad]

Dear PoisonAlien,

I want to use silent variants but removeSilent is not working for latest install of maftools. It produces following error.

Error in read.maf(maf = "3_UTR.maf", removeSilent = FALSE, useAll = FALSE) : unused argument (removeSilent = FALSE).

I have installed it on another system a week ago and it was working perfectly.

[PoisonAlien]

Hi,

I recently made a lots of changes to maftools including to read.maf. In recent version synonymous variants will be kept in a separate slot and won't be mixed with non-synonymous variants. May I ask the purpose you're doing this for ? so that I can make changes if it makes sense. Is it only for plotting ?

[Naziaahmad]

Thank you for prompt reply.

Actually I want to check density and recurrency of mutations in 3' UTR region of top genes.

Regards,

Nazia

On Sep 19, 2017 5:02 PM, "PoisonAlien" notifications@github.com wrote:

Hi,

I recently made a lots of changes to maftools including to read.maf. In recent version synonymous variants will be kept in a separate slot and won't be mixed with non-synonymous variants. May I ask the purpose you're doing this for ? so that I can make changes if it makes sense. Is it only for plotting ?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/PoisonAlien/maftools/issues/63#issuecomment-330461507, or mute the thread https://github.com/notifications/unsubscribe-auth/AemqLvonbOSCtBqEyVPMn3PPJxxB5TPqks5sj3UKgaJpZM4Pb_XH .

[PoisonAlien]

Ah! Okay.. So this is only to get sample/gene summary statistics isn't it ?

[Naziaahmad]

Yes

On Sep 19, 2017 5:20 PM, "PoisonAlien" notifications@github.com wrote:

Ah! Okay.. So this is only to get sample/gene summary statistics isn't it ?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/PoisonAlien/maftools/issues/63#issuecomment-330465802, or mute the thread https://github.com/notifications/unsubscribe-auth/AemqLob1OPgEqKf4BHmE0nUeaRNsDSgyks5sj3lkgaJpZM4Pb_XH .

[PoisonAlien]

Hi, Can you install from github again. I have put new function mafSummary and it should get you what you're looking for. Please let me know if this is what you wanted.

[Naziaahmad]

Thank you so much.

It really worked exactly what i want.

Another suggestion is to add mutated sample per variant classification along with the total mutated sample.

Thank you.

Regards,

Nazia

On Sep 19, 2017 6:06 PM, "PoisonAlien" notifications@github.com wrote:

Reopened #63 https://github.com/PoisonAlien/maftools/issues/63.

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[MBeyens]

Hi, I would like to plot the full summary of a cohort, so not only the limited defined categories in maftools; but also UTR's, intronic etc.
Is there a way to do so? Like the plot plotmafSummary, but all then?

Thank you in advance!

[PoisonAlien]

Hi, Sorry for late reply. You can include desired variant classifications in the plot. By default maftools uses variant Classifications with High/Moderate variant consequences as non-syn variant. You can provide a separate list via argument vc_nonSyn while reading maf with read.maf and it should do the trick.

[ghost]

Hi, same as @MBeyens, I wanted to plot every variant regardless of annotation. But read.maf does not recognize vc_nonSyn argument, any idea why? Thanks so much!

[PoisonAlien]

Hi, What version of maftools are you using ? Could you post your session info and read.maf command ?

[ghost]

Thanks for the reply. Below is the information:

source("https://bioconductor.org/biocLite.R") Bioconductor version 3.5 (BiocInstaller 1.26.1), ?biocLite for help A newer version of Bioconductor is available for this version of R, ?BiocUpgrade for help biocLite("maftools") BioC_mirror: https://bioconductor.org Using Bioconductor 3.5 (BiocInstaller 1.26.1), R 3.4.1 (2017-06-30). Installing package(s) ‘maftools’ trying URL 'https://bioconductor.org/packages/3.5/bioc/bin/macosx/el-capitan/contrib/3.4/maftools_1.2.30.tgz' Content type 'application/x-gzip' length 6329045 bytes (6.0 MB)

Command

laml <- read.maf(maf = var.annovar.maf,vc_nonSyn=c("UNKNOWN")) Error in read.maf(maf = var.annovar.maf, vc_nonSyn = c("UNKNOWN")) : unused argument (vc_nonSyn = c("UNKNOWN"))

[PoisonAlien]

Hi, You're still using older version of maftools (1..2.30). Current version is 1.4.05 Please update and try again, it should work.

[ghost]

Thank you, it worked.