Question: Info Score > 1 Plink?
0
gravatar for bg1116
4 months 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 • 243 views
ADD COMMENTlink modified 4 months ago by chrchang5234.3k • written 4 months 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 4 months ago by Kevin Blighe33k

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 4 months ago • written 4 months ago by chrchang5234.3k
1
gravatar for chrchang523
4 months ago by
chrchang5234.3k
United States
chrchang5234.3k 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 4 months ago • written 4 months ago by chrchang5234.3k
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