error on testing the package

[aheravi]

Hi,
I'm getting an error in testing your package based on the tutorial you've provided here:
https://cran.r-project.org/web/packages/mutSignatures/vignettes/get_sarted_with_mutSignatures.html

# Attach context
x <- attachContext(mutData = x,chr_colName = "CHROM",start_colName = "POS", end_colName = "POS",nucl_contextN = 3,BSGenomeDb = hg19)

An error has occurred!

And here is part of my sessioninfo():

other attached packages:
 [1] mutSignatures_2.1.1               foreach_1.5.2                    
 [3] BSgenome.Hsapiens.UCSC.hg19_1.4.3 BSgenome_1.62.0                  
 [5] rtracklayer_1.54.0                Biostrings_2.62.0                
 [7] XVector_0.34.0                    GenomicRanges_1.46.1             
 [9] GenomeInfoDb_1.30.1               IRanges_2.28.0                   
[11] S4Vectors_0.32.3                  BiocGenerics_0.40.0              
[13] gridExtra_2.3                     ggplot2_3.4.0                    
[15] kableExtra_1.3.4                  reshape2_1.4.4                   
[17] dplyr_1.0.8       

Could you please comment on that?
Thanks,
Ali

[dami82]

You are using an outdated version of mutSignatures (2.1.1). Please install the latest version from github (2.1.5) and try again. Let me know if the error persists.Best regards,Damiano——Damiano FantiniSent from my iPhoneOn Feb 2, 2023, at 18:39, aheravi ***@***.***> wrote: Hi, I'm getting an error in testing your package based on the tutorial you've provided here: https://cran.r-project.org/web/packages/mutSignatures/vignettes/get_sarted_with_mutSignatures.html # Attach context x <- attachContext(mutData = x,chr_colName = "CHROM",start_colName = "POS", end_colName = "POS",nucl_contextN = 3,BSGenomeDb = hg19) An error has occurred! And here is part of my sessioninfo(): other attached packages: [1] mutSignatures_2.1.1 foreach_1.5.2 [3] BSgenome.Hsapiens.UCSC.hg19_1.4.3 BSgenome_1.62.0 [5] rtracklayer_1.54.0 Biostrings_2.62.0 [7] XVector_0.34.0 GenomicRanges_1.46.1 [9] GenomeInfoDb_1.30.1 IRanges_2.28.0 [11] S4Vectors_0.32.3 BiocGenerics_0.40.0 [13] gridExtra_2.3 ggplot2_3.4.0 [15] kableExtra_1.3.4 reshape2_1.4.4 [17] dplyr_1.0.8 Could you please comment on that? Thanks, Ali —Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[aheravi]

Hi Damiano, Thanks for your prompt reply. Yes that resolved the issue. On a different note, do you think I can reformat the mutation data I have, below, to be used in your package? I don't have the VCF files. Thanks, Ali sample chr start end reference alt gene effect Amino_Acid_Change DNA_VAF SIFT PolyPhen T1 10 123810032 123810032 A C TACC2 Missense_Mutation p.T38M 0.88 benign(0.335)

…

________________________________ From: Damiano Fantini ***@***.***> Sent: Thursday, February 2, 2023 6:20 PM To: dami82/mutSignatures Cc: Alireza Heravi Moussavi; Author Subject: Re: [dami82/mutSignatures] error on testing the package (Issue #17) You are using an outdated version of mutSignatures (2.1.1). Please install the latest version from github (2.1.5) and try again. Let me know if the error persists.Best regards,Damiano--Damiano FantiniSent from my iPhoneOn Feb 2, 2023, at 18:39, aheravi ***@***.***> wrote:? Hi, I'm getting an error in testing your package based on the tutorial you've provided here: https://cran.r-project.org/web/packages/mutSignatures/vignettes/get_sarted_with_mutSignatures.html # Attach context x <- attachContext(mutData = x,chr_colName = "CHROM",start_colName = "POS", end_colName = "POS",nucl_contextN = 3,BSGenomeDb = hg19) An error has occurred! And here is part of my sessioninfo(): other attached packages: [1] mutSignatures_2.1.1 foreach_1.5.2 [3] BSgenome.Hsapiens.UCSC.hg19_1.4.3 BSgenome_1.62.0 [5] rtracklayer_1.54.0 Biostrings_2.62.0 [7] XVector_0.34.0 GenomicRanges_1.46.1 [9] GenomeInfoDb_1.30.1 IRanges_2.28.0 [11] S4Vectors_0.32.3 BiocGenerics_0.40.0 [13] gridExtra_2.3 ggplot2_3.4.0 [15] kableExtra_1.3.4 reshape2_1.4.4 [17] dplyr_1.0.8 Could you please comment on that? Thanks, Ali

-Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you are subscribed to this thread.Message ID: ***@***.***> - Reply to this email directly, view it on GitHub<#17 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ACEEQXQK3EWL2ZJXIOH5OYDWVRTPDANCNFSM6AAAAAAUPUI2HA>. You are receiving this because you authored the thread.Message ID: ***@***.***>

[dami82]

Yes! This data format should be compatible with mutSignatures. Have a look at the vignette and make sure to set the right arguments (to match the colNames of your data.frame).
Best regards.

[cyrusmallon]

Hi,
The latest version (v2.1.5) doesn't appear to be on CRAN. Should it be?
Cheers,
Cyrus

[dami82]

Good point.It probably should. I just like GitHub better and tend to forget about CRAN.Best regards,Damiano——Damiano FantiniSent from my iPhoneOn Feb 15, 2023, at 13:19, Cyrus A. Mallon ***@***.***> wrote: Hi, The latest version (v2.1.5) doesn't appear to be on CRAN. Should it be? Cheers, Cyrus —Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you commented.Message ID: ***@***.***>

[aheravi]

Hi @dami82,
To use my mutation data and as I don't have some info based on the tutorial, I am assigning constant values to the following columns as below. Just wondering if that would be safe to do for using your tool to extract my mutation signatures.

QUAL = 30
FILTER = .
INFO = .
FORMAT = GT:PL
XTR1 = 0/1

Thanks.

[dami82]

Thanks for your interest and for your question.Those columns are typically found in a VCF file but they are not used by mutSignatures. So, you don't even need to create them. Best regards,Damiano——Damiano FantiniSent from my iPhoneOn Apr 13, 2023, at 18:17, aheravi ***@***.***> wrote: Hi @dami82, To use my mutation data and as I don't have some info based on the tutorial, I am assigning constant values to the following columns as below. Just wondering if that would be safe to do for using your tool to extract my mutation signatures. QUAL = 30 FILTER = . INFO = . FORMAT = GT:PL XTR1 = 0/1 Thanks. —Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you were mentioned.Message ID: ***@***.***>