.assoc.logistic
Multi-covariate logistic regression from --logistic. BETA column appears with '--logistic beta'; otherwise OR. With --ci 0.xy, SE, L_xy, U_xy are inserted before STAT (SE is on log-odds scale).
Overview
| Field |
Value |
| Format key |
plink_logistic |
| Spec file |
formats/plink_logistic.json |
| Cite name |
PLINK 1.9 |
| Version |
PLINK 1.9 (doc revision 19 Aug 2025) |
| Last checked |
20260326 |
| Source |
https://www.cog-genomics.org/plink/1.9/formats#assoc_linear |
| Citation |
Purcell, S., Neale, B., Todd-Brown, K., Thomas, L., Ferreira, M. A., Bender, D., ... & Sham, P. C. (2007). PLINK: a tool set for whole-genome association and population-based linkage analyses. The American journal of human genetics, 81(3), 559-575. |
| ## File layout |
|
| Field |
Value |
| Separator |
TAB |
| Header row |
yes |
| Column order |
CHR, SNP, BP, A1, TEST, NMISS, OR, BETA, SE, L95, U95, STAT, P |
| ## Column mapping |
|
| Raw header |
Canonical |
Canonical (secondary) |
A1 |
EA |
— |
A2 |
NEA |
— |
BETA |
BETA |
— |
BP |
POS |
— |
CHISQ |
CHISQ |
— |
CHR |
CHR |
— |
L95 |
OR_95L |
— |
NMISS |
N |
— |
OR |
OR |
— |
P |
P |
— |
SE |
SE |
— |
SNP |
SNPID |
rsID |
STAT |
T |
— |
TEST |
— |
— |
U95 |
OR_95U |
— |
| ## Header descriptions |
|
|
| Column |
Description |
A1 |
Allele 1 (omitted with 'no-snp') |
A2 |
Allele 2 (when present) |
BETA |
Log-odds coefficient ('--logistic beta') |
BP |
Base-pair coordinate (omitted with 'no-snp') |
CHISQ |
Chi-square (when reported for some tests) |
CHR |
Chromosome code (omitted with 'no-snp') |
L95 |
Lower end of symmetric approx. CI for OR (--ci) |
NMISS |
Observations with nonmissing genotype, phenotype, and covariates |
OR |
Odds ratio (without '--logistic beta') |
P |
Asymptotic p-value for t-statistic |
SE |
Standard error of beta / log-odds (--ci) |
SNP |
Variant identifier (omitted with 'no-snp') |
STAT |
t-statistic |
TEST |
Test identifier |
U95 |
Upper end of symmetric approx. CI for OR (--ci) |
| ## Coverage |
|
7/9 tier groups satisfied.
| Tier |
Status |
Matched |
Missing |
| Variant ID |
yes |
SNPID, rsID |
— |
| Genomic location |
yes |
CHR, POS |
— |
| Effect / other allele |
yes |
EA, NEA |
— |
| Effect size |
yes |
BETA, OR |
HR, Z |
| Uncertainty |
yes |
SE |
— |
| P-value |
yes |
P |
MLOG10P |
| Sample size |
yes |
N |
N_CASE |
| Allele frequency |
no |
— |
EAF, MAF, NEAF |
| Imputation / QC |
no |
— |
INFO |
| ## See also |
|
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