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deconstructSigs
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mut.to.sigs.input Error in GrCH38 #19

Closed mgala81 closed 7 years ago

mgala81 commented 7 years ago

test4.txt

Certain genomic profiles are generating the error: Error in if (trimer %in% all.tri) { : argument is of length zero

I'm using the appropiate BSgenome object. I've attached a sample input file. I tried adding a check to see if trimer was not null prior, but that ended up creating a blank matrix.

mgala81 commented 7 years ago

Hi- I attached a file to the thread called test4.txt which the input. The second sample from TCGA (2 total) is causing the error. The first sample when done alone creates no issue.

Best,

Manish

From: raerose01 [notifications@github.com] Sent: Thursday, June 22, 2017 3:44 PM To: raerose01/deconstructSigs Cc: Gala, Manish K.; Author Subject: Re: [raerose01/deconstructSigs] mut.to.sigs.input Error in GrCH38 (#19)

Hi, do you have an example of what's causing the error?

On Thu, Jun 22, 2017 at 7:34 PM, mgala81 notifications@github.com wrote:

Certain genomic profiles are generating the error:

Error in if (trimer %in% all.tri) { : argument is of length zero

I'm using the appropiate BSgenome object.

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mgala81 commented 7 years ago

Here is the file again if not seen. test4.txt

raerose01 commented 7 years ago

Ok, I think it should be fixed now. At least, that file ran for me. But you should re-install the package from the GitHub site. And if it still doesn't work, can you try changing the first column name to be "Sample" and let me know? Something odd was failing earlier.

mgala81 commented 7 years ago

Many thanks, it works well now!

From: raerose01 [notifications@github.com] Sent: Thursday, June 22, 2017 4:36 PM To: raerose01/deconstructSigs Cc: Gala, Manish K.; Author Subject: Re: [raerose01/deconstructSigs] mut.to.sigs.input Error in GrCH38 (#19)

Ok, I think it should be fixed now. At least, that file ran for me. But you should re-install the package from the GitHub site. And if it still doesn't work, can you try changing the first column name to be "Sample" and let me know? Something odd was failing earlier.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/raerose01/deconstructSigs/issues/19#issuecomment-310495241, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AcQ_XnSIzsr2CtKK-JYJggmnk06Q9dk4ks5sGtAygaJpZM4OCraX.

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.