best way to convert SNP genotype to numeric matrix

[qgao2]

Hi Xiaolei,
thanks a lot for writing this nice package.
I would like to use MVP for my project, but I am not sure the best way to convert unphased SNP genotype (vcf format, around 60k SNPs) to numeric matrix (0,1,2). Do you which tool I should use to do the conversion.

[XiaoleiLiuBio]

I have written some codes for converting vcf to numeric, I will update the function in MVP soon.

[qgao2]

Nice! Thank you, XiaoLei.

…

On Fri, Nov 10, 2017 at 2:00 AM, Xiaolei Liu ***@***.***> wrote: I have written some codes for converting vcf to numeric, I will update the function in MVP soon. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#9 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AM_4lc0ymYDHX_2bzUimP8L3jINl5TMBks5s1AKOgaJpZM4QU5hD> .

[hyacz]

The code for converting vcf to numeric has been added to MVP some time ago. You can use the following code to get a 012-encoded genotype matrix in big.matrix format.

MVP.Data.VCF2MVP(fileVCF="my.vcf", out="my.mvp", threads=1)
geno <- attach.big.matrix("my.mvp.geno.desc")

1. big.matrix is mostly similar to base::matrix , if you want a real base::matrix you can use the following code:

geno <- geno[]

2. If you really need a 012-encoded genotype matrix text file, you can look at the write.big.matrix in the bigmemory package, which accepts a big.matrix

MVP.Data.VCF2MVP(fileVCF="my.vcf", out="my.mvp", threads=1)
geno <- attach.big.matrix("my.mvp.geno.desc")
write.big.matrix(geno, "my.numeric", sep=" ")

[hyacz]

This issue is closed because it is no longer active.