Thanks for making such kinds of videos. Could you please make video of tumor and normal sample variant calling in vcf files and conversion of vcf files to maf filed?
Thanks for the information. How to visulaize CNV amplification data like how can i add amplification status like Amplification or Loss inside the input file? and amplificaation status want to see along with SNV.
Hey, Thanks for your work and efforts...But pls can you give a detailed explanation on how to convert vcf to maf file (maybe make a video and attach link to the reply). The link you suggested uses another programming language(?) Perl, and some of us are not familiar with that. And yes i have looked on how to run perl scripts in R studio but it crashes...when i attempt. Thanks in advance.
For reference do you mean this package specifically? I think their documentation is the best way to under the logic behind each of their function www.bioconductor.org/packages/devel/bioc/vignettes/maftools/inst/doc/maftools.html
Thanks for great tutorial. This is an example of reading TCGA-LAML data from maftools. laml.maf = system.file('extdata', 'tcga_laml.maf.gz', package = 'maftools') laml.clin = system.file('extdata', 'tcga_laml_annot.tsv', package = 'maftools') laml = read.maf(maf = laml.maf, clinicalData = laml.clin) This example worked well. I want to analyze melanoma data, so I changed skcm.maf = system.file('extdata', 'tcga_skcm.maf.gz', package = 'maftools') but it does not work well. Please let me know if you know how to solve this problem.
system.file() only extract files that exists in the package, if you need the TCGA-SKCM, you might need to download the file directly from TCGA using the TCGAbiolinks package. I have paste an example code here, but you will still need to check the GDC portal for the exact file available on the database I have also another video explaining how to download the data here (ruclips.net/video/z36fu178jIQ/видео.html), check the preparing data section. query
Thanks a lot for the tutorial. I have a question related to another TCGA cohort which is TCGA-LUAD. I am interested in exploring differences between KRAS+ LUAD and KRAS wild-type LUAD. I have downloaded the MAF file and filtered it to contain only KRAS mutations and I got 163 KRAS mutated samples. Then I downloaded the gene expression data for the whole cohort (around 537 samples). To perform the analyses I need to divide the 537 samples into two groups; KRAS+ and KRAS wild type. I know that from the 537 samples I have 163 KRAS mutated samples (from the MAF file), but what about the remaining 374 samples? Can I consider them as KRAS wild type because they are not available within the MAF file? or does this mean that we don't know their mutation status because they are not tested for the KRAS mutation? is there any way through which I can get the samples that don't contain the KRAS mutation (wild type)? Many thanks in advance
To be really honest I am not very familiar with this cohort and this specific mutation you are working on. In theory those that have not shown the mutation can be treated as wildtype since it is not detected in the sequencing data from the patients. For KRAS in TCGA-LUAD however, I am not too confident to say, just that, in general this should be the case.
system.file() will load the file that are contained in the package. since you already have the maf files in the current dir, you can simply load in the maf tools using the normal readmaf() function, try this (just make sure your filename is exactly "oc.maf.gz" oral
![How to check the frequencies of gene mutations in TCGA cancer database [R]](http://i.ytimg.com/vi/5kf2DniD1No/mqdefault.jpg)
![How to check the frequencies of gene mutations in TCGA cancer database [R]](/img/tr.png)
Thanks for making such kinds of videos. Could you please make video of tumor and normal sample variant calling in vcf files and conversion of vcf files to maf filed?
Very good, thank you!
Thanks for the information. How to visulaize CNV amplification data like how can i add amplification status like Amplification or Loss inside the input file? and amplificaation status want to see along with SNV.
Hey,
Thanks for your work and efforts...But pls can you give a detailed explanation on how to convert vcf to maf file (maybe make a video and attach link to the reply). The link you suggested uses another programming language(?) Perl, and some of us are not familiar with that. And yes i have looked on how to run perl scripts in R studio but it crashes...when i attempt. Thanks in advance.
Thanks for the tutorial, and it is really helpful. Since I am a beginner, could you provide some more information for reference?
For reference do you mean this package specifically? I think their documentation is the best way to under the logic behind each of their function
www.bioconductor.org/packages/devel/bioc/vignettes/maftools/inst/doc/maftools.html
Thanks for great tutorial.
This is an example of reading TCGA-LAML data from maftools.
laml.maf = system.file('extdata', 'tcga_laml.maf.gz', package = 'maftools')
laml.clin = system.file('extdata', 'tcga_laml_annot.tsv', package = 'maftools')
laml = read.maf(maf = laml.maf, clinicalData = laml.clin)
This example worked well.
I want to analyze melanoma data, so I changed skcm.maf = system.file('extdata', 'tcga_skcm.maf.gz', package = 'maftools') but it does not work well.
Please let me know if you know how to solve this problem.
system.file() only extract files that exists in the package, if you need the TCGA-SKCM, you might need to download the file directly from TCGA using the TCGAbiolinks package.
I have paste an example code here, but you will still need to check the GDC portal for the exact file available on the database
I have also another video explaining how to download the data here (ruclips.net/video/z36fu178jIQ/видео.html), check the preparing data section.
query
Thanks a lot for the tutorial. I have a question related to another TCGA cohort which is TCGA-LUAD. I am interested in exploring differences between KRAS+ LUAD and KRAS wild-type LUAD. I have downloaded the MAF file and filtered it to contain only KRAS mutations and I got 163 KRAS mutated samples.
Then I downloaded the gene expression data for the whole cohort (around 537 samples). To perform the analyses I need to divide the 537 samples into two groups; KRAS+ and KRAS wild type. I know that from the 537 samples I have 163 KRAS mutated samples
(from the MAF file), but what about the remaining 374 samples?
Can I consider them as KRAS wild type because they are not available within the MAF file? or does this mean that we don't know their mutation status because they are not tested for the KRAS mutation? is there any way through which I can get the samples that don't contain the KRAS mutation (wild type)?
Many thanks in advance
To be really honest I am not very familiar with this cohort and this specific mutation you are working on. In theory those that have not shown the mutation can be treated as wildtype since it is not detected in the sequencing data from the patients.
For KRAS in TCGA-LUAD however, I am not too confident to say, just that, in general this should be the case.
Thank you for the reply. Much appreciated!
Hi,
i am using the below commands:
>icgc =system.file("extdata", "ssm_orca_In.tsv.gz", package="maftools")
>maf
may be update the library
oral
Hi it seems the "oc.maf.gz" does not exist in the package I downloaded from Bioconductor. did you download this maf from external sources?
@@LiquidBrain I already have this maf file in the working directory.
system.file() will load the file that are contained in the package. since you already have the maf files in the current dir, you can simply load in the maf tools using the normal readmaf() function, try this (just make sure your filename is exactly "oc.maf.gz"
oral
againt the GDC is upgraded so your code is not supportive now
Thank you for your work!
It is possible to upload the R file and link for the data?
oops, you can check out the script here:
github.com/brandonyph/LiquidBrain_Scripts
@@LiquidBrain thank you!! :3