how to import/read .vcf files in R

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how to import/read .vcf files in R

anikaM
Hello,

I tried doing:
> library(vcfR)
> vcf <- read.vcfR("ALL.chr1.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf", verbose = FALSE )

but this takes forever to load and I am not sure it is even working.

Any other suggestion on how I can read in .vcf file in R?

Thanks
Ana

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Re: how to import/read .vcf files in R

Bert Gunter-2
As this apparently involves genomic data, I would suggest that you ask this
on the BioConductor site:
https://www.bioconductor.org/help/
especially if you don't get effective help here.

Bert Gunter




On Tue, Jan 28, 2020 at 9:29 AM Ana Marija <[hidden email]>
wrote:

> Hello,
>
> I tried doing:
> > library(vcfR)
> > vcf <-
> read.vcfR("ALL.chr1.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf",
> verbose = FALSE )
>
> but this takes forever to load and I am not sure it is even working.
>
> Any other suggestion on how I can read in .vcf file in R?
>
> Thanks
> Ana
>
> ______________________________________________
> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

        [[alternative HTML version deleted]]

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and provide commented, minimal, self-contained, reproducible code.
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Re: how to import/read .vcf files in R

anikaM
Thanks for the tip!

On Tue, Jan 28, 2020 at 11:36 AM Bert Gunter <[hidden email]> wrote:

>
> As this apparently involves genomic data, I would suggest that you ask this on the BioConductor site:
> https://www.bioconductor.org/help/
> especially if you don't get effective help here.
>
> Bert Gunter
>
>
>
>
> On Tue, Jan 28, 2020 at 9:29 AM Ana Marija <[hidden email]> wrote:
>>
>> Hello,
>>
>> I tried doing:
>> > library(vcfR)
>> > vcf <- read.vcfR("ALL.chr1.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf", verbose = FALSE )
>>
>> but this takes forever to load and I am not sure it is even working.
>>
>> Any other suggestion on how I can read in .vcf file in R?
>>
>> Thanks
>> Ana
>>
>> ______________________________________________
>> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.