TCGA - Including copy number data into oncoplots

[LeaLe88]

Good afternoon,

I have been trying to include copy number data into oncoplots following this instructions (section 0.3.2 (Custum copy-number table)) since I do not have GISTIC results for the TCGA KIRC cohort.

https://www.bioconductor.org/packages/devel/bioc/vignettes/maftools/inst/doc/oncoplots.html#032_Custom_copy-number_table

However, in the last step I keep getting the following error:

kirc.plus.cn = read.maf(maf = kirc,
                       cnTable = custom.cn.data,
                         verbose = FALSE) 
Error in file.info(file) : invalid filename argument

Has anyone an idea what I can do?

The same issue was described here: #871

Previously I have downloaded the TCGA KIRC data and have KIRC_TCGA_gene-level-cnv.RDS, KIRC_TCGA_snv.maf, KIRC_TCGA_snv.maf.RDS, etc. available.

Thank you !

[PoisonAlien]

Hi,

Is custom.cn.data a data.frame or a file path?

[LeaLe88]

I tried both as I read somewhere that it should be a file path:
As dataframe:
kirc.plus.cn = read.maf(maf = kirc,
cnTable = custom.cn.data,
verbose = FALSE)

With Path:
kirc.plus.cn = read.maf(maf = kirc,
cnTable = "/...path.../custom.cn.data.txt",verbose=FALSE)

[PoisonAlien]

I am having a hard time reproducing the issue. It works fine with input as a data.frame and a file.
Could you please share the custom.cn.data.txt?

[LeaLe88]

Sure, I only made it for one gene as a test.
custom.cn.data.txt

[LeaLe88]

I am trying to load my MAF file in above comment in zip, but I think it is not uploading

[LeaLe88]

any more ideas? thank you!

[PoisonAlien]

Could you please email me a reproducible MAF if possible? You can remove all sensitive information and change sample names if you'd like.

[LeaLe88]

Thank you so much for your reply. I will email it to you now. It is from TCGA, so no problem with sensitive information.

[PoisonAlien]

Hi,

Thank you for the data. I will answer here so that we can keep things in the chain. I tried with your data and it went through normally without any errors.

> m = maftools::read.maf(maf = "~/Downloads/rstudio-export/KIRC_TCGA_filtered_snv.maf", cnTable = "~/Downloads/rstudio-export/custom.cn.data.txt")
-Reading
-Validating
-Silent variants: 5150 
-Processing copy number data
-Summarizing
--Mutiple centers found
BI;BCM;BCM;BI--Possible FLAGS among top ten genes:
  TTN
  MUC16
-Processing clinical data
--Missing clinical data
-Finished in 1.941s elapsed (1.618s cpu) 

> m
An object of class  MAF 
                        ID       summary        Mean Median
 1:             NCBI_Build        GRCh38          NA     NA
 2:                 Center BI;BCM;BCM;BI          NA     NA
 3:                Samples           351          NA     NA
 4:                 nGenes          9128          NA     NA
 5:                DeepDel            86  0.24501425      0
 6:        Frame_Shift_Del          1710  4.87179487      4
 7:        Frame_Shift_Ins           506  1.44159544      1
 8:           In_Frame_Del           248  0.70655271      0
 9:           In_Frame_Ins            21  0.05982906      0
10:      Missense_Mutation         13379 38.11680912     34
11:      Nonsense_Mutation          1010  2.87749288      2
12:       Nonstop_Mutation            24  0.06837607      0
13:             ShallowAmp            96  0.27350427      0
14:            Splice_Site           468  1.33333333      1
15: Translation_Start_Site            27  0.07692308      0
16:                  total         17575 50.07122507     46
17:                    Amp            77  0.21937322      0
18:                    Del            92  0.26210826      0
19:              CNV_total           169  0.48148148      0

Maybe you could try updating the package?

[LeaLe88]

Good afternoon, Thank you so much for sharing your code adding "maftools::" in front of read.maf actually solved my problem!! I have loaded it now. I hope you dont mind if I ask you two additional questions which I cant find an answer to. 1) It was described under 0.3.2 ( https://www.bioconductor.org/packages/devel/bioc/vignettes/maftools/inst/doc/oncoplots.html#032_Custom_copy-number_table) that a "*random* CN status for above samples" is created. Now I am wondering if this example is only for demonstration and I cant not actually use the created copy-number table for my *actual analysis*? 2) I would like to combine my newly KIRC_TCGA_filtered_met450.RDS.zip <https://drive.google.com/file/d/1MLRYsZtVM3j0s5DoV7yPVbKwc7A40dzb/view?usp=drive_web> created MAF file also with the methylation data from TCGA (please find the file attached). Do you have any idea how I can merge them? Thank you again for your help, very appreciated. Best Regards, Lea

…

On Wed, 8 Nov 2023 at 20:11, Anand Mayakonda ***@***.***> wrote: Hi, Thank you for the data. I will answer here so that we can keep things in the chain. I tried with your data and it went through normally without any errors. > m = maftools::read.maf(maf = "~/Downloads/rstudio-export/KIRC_TCGA_filtered_snv.maf", cnTable = "~/Downloads/rstudio-export/custom.cn.data.txt")-Reading-Validating-Silent variants: 5150 -Processing copy number data-Summarizing--Mutiple centers foundBI;BCM;BCM;BI--Possible FLAGS among top ten genes: TTN MUC16-Processing clinical data--Missing clinical data-Finished in 1.941s elapsed (1.618s cpu) > mAn object of class MAF ID summary Mean Median 1: NCBI_Build GRCh38 NA NA 2: Center BI;BCM;BCM;BI NA NA 3: Samples 351 NA NA 4: nGenes 9128 NA NA 5: DeepDel 86 0.24501425 0 6: Frame_Shift_Del 1710 4.87179487 4 7: Frame_Shift_Ins 506 1.44159544 1 8: In_Frame_Del 248 0.70655271 0 9: In_Frame_Ins 21 0.05982906 010: Missense_Mutation 13379 38.11680912 3411: Nonsense_Mutation 1010 2.87749288 212: Nonstop_Mutation 24 0.06837607 013: ShallowAmp 96 0.27350427 014: Splice_Site 468 1.33333333 115: Translation_Start_Site 27 0.07692308 016: total 17575 50.07122507 4617: Amp 77 0.21937322 018: Del 92 0.26210826 019: CNV_total 169 0.48148148 0 Maybe you could try updating the package? — Reply to this email directly, view it on GitHub <#985 (reply in thread)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AQ6IZRZF6QWHAQEDSTSCYT3YDPKNLAVCNFSM6AAAAAA64PFT46VHI2DSMVQWIX3LMV43SRDJONRXK43TNFXW4Q3PNVWWK3TUHM3TKMJUGQZTQ> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[PoisonAlien]

Hi,

I am glad it worked. It seems that you forgot to load the library before reading the MAF file.

1. Yes, you can use your file as a copy number source. The vignette shows dummy data just as an example.
2. It is not possible to merge methylation data with MAF.

[LeaLe88]

Hello, Thank you for your response. Regarding 2 however I saw TCGA oncoplots, which contained mutations, deletions and methylation data. I assume that somehow the data was merged. Thank you anyway! Best Regards, Lea

…

On Thu, 9 Nov 2023 at 15:31, Anand Mayakonda ***@***.***> wrote: Hi, I am glad it worked. It seems that you forgot to load the library before reading the MAF file. 1. Yes, you can use your file as a copy number source. The vignette shows dummy data just as an example. 2. It is not possible to merge methylation data with MAF. — Reply to this email directly, view it on GitHub <#985 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AQ6IZR4JILT3NV7HBGFCGFLYDTSLBAVCNFSM6AAAAAA64PFT46VHI2DSMVQWIX3LMV43SRDJONRXK43TNFXW4Q3PNVWWK3TUHM3TKMRTGE2TK> . You are receiving this because you authored the thread.Message ID: ***@***.***>