Question: How to force missing values for genotype?
1
gravatar for aritra90
12 months ago by
aritra9060
United States
aritra9060 wrote:

Hi,

I was wondering how to force missing values in genotypes in PLINK format files?

I tried doing --update-alleles followed by --recode but that didn't work. I want to force some arbitrarily chosen marker's genotype values for some individuals to 0 (missing). In other words, I want to mask them for imputation (such that, doing --missing will increase the missingness rate for the chosen marker)

I am not sure how to achieve this using PLINK. It'd be great if anyone has any idea on how to go about doing this.

genotypes snp plink • 520 views
ADD COMMENTlink modified 12 months ago by zx87549.1k • written 12 months ago by aritra9060
2
gravatar for chrchang523
12 months ago by
chrchang5236.7k
United States
chrchang5236.7k wrote:

See the Plink manual : Set blocks of genotype calls to missing

Set blocks of genotype calls to missing
--zero-cluster <filename>

If clusters have been defined, --zero-cluster takes a file with variant IDs in the first column and cluster IDs in the second, and sets all the corresponding genotype calls to missing. See the PLINK 1.07 documentation for an example.

This flag must now be used with --make-bed and no other output commands (since PLINK no longer keeps the entire genotype matrix in memory).

ADD COMMENTlink modified 12 months ago by zx87549.1k • written 12 months ago by chrchang5236.7k
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