Question: Missing data in covariate file in PLINK
0
gravatar for landscape95
16 months ago by
landscape95170
landscape95170 wrote:

Hi everyone, I am doing the summary statistics for SNP association in Plink. However, the program says I have missing values even though I have checked the phenotype information, it doesn't have -9/0/NA values. When I checked the covariate file, some values had -9/0 values, these values are the true values, they are not annotated as missing, may I ask how can I flag another value for the covariate file only? I don't want it effect my phenotype missing values which can be -9/0/NA in my future work. Your help is really appreciated!

gwas • 958 views
ADD COMMENTlink modified 16 months ago by karl.stamm3.6k • written 16 months ago by landscape95170
1
gravatar for karl.stamm
16 months ago by
karl.stamm3.6k
United States
karl.stamm3.6k wrote:

PLINK v1.9 has a parameter --missing-phenotype which lets you assign a number other than -9 as the key for missing value. see their docs for encoding parameters https://www.cog-genomics.org/plink/1.9/input#pheno

ADD COMMENTlink written 16 months ago by karl.stamm3.6k

Thank you very much! I have read this document but according to it, the --missing-phenotype will be applied across all phenotype-related data, the .fam file will also be considered the same. I wish that I could assign the missing phenotype differently between the .bim file and the covariate file. Is there any way that I can do it? Thank you!

ADD REPLYlink modified 16 months ago • written 16 months ago by landscape95170

I don't know what your .bim is, but you should be able to recode any file, or just run the software separately for each condition. I gather PLINK is just running one column of the phenotype file anyway, you'll be doing separate analyses. You're trying to do several analyses right now with incompatible annotation files. Re-generate the BIM to match the phenotypes, or vice versa.

ADD REPLYlink written 16 months ago by karl.stamm3.6k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1566 users visited in the last hour