Question: Info Score > 1 Plink?
0
gravatar for bg1116
10 weeks ago by
bg11160
bg11160 wrote:

What does an info score > 1 mean? I thought all scores should be between 0 and 1. Info score comes from assoc.dosage file in plink.

score plink gwas • 165 views
ADD COMMENTlink modified 10 weeks ago by chrchang5233.9k • written 10 weeks ago by bg11160

did you check the plink manual pages:

The fields INFO and NPRX refer to how well PLINK managed, if at all, to impute the SNP. If NPRX is zero, then it could not be even poorly imputed. If INFO ranges from between 0 and 1, although it can be greater than 1 occasionally. A higher value general means a better imputed SNP; roughly speaking, only looking at imputed SNPs with a INFO value greater than 0.8 or so is probably good practice. More specific details on these metrics will be posted soon.

...I put in bold the important line.

Kevin

ADD REPLYlink written 10 weeks ago by Kevin Blighe30k

INFO has the same meaning in both files, but that documentation snippet is actually for a slightly different (and defunct) command, --proxy-assoc instead of --dosage.

ADD REPLYlink modified 10 weeks ago • written 10 weeks ago by chrchang5233.9k
1
gravatar for chrchang523
10 weeks ago by
chrchang5233.9k
United States
chrchang5233.9k wrote:

The INFO field in an .assoc.dosage file contains the MaCH r-squared imputation quality metric, which is [observed dosage variance] / [expected variance, given observed allele frequencies and Hardy-Weinberg equilibrium]. Despite the r-squared name, this is not guaranteed to be less than or equal to 1, especially when there's significant deviation from Hardy-Weinberg equilibrium; but low values can still be trusted to correspond to poorly-imputed SNPs.

ADD COMMENTlink modified 10 weeks ago • written 10 weeks ago by chrchang5233.9k
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