glm sample size vs OBS_CT

[Mariona Bustamante]

Dear all,

I am running glm with plink2. See code below:

PLINK v2.00a3.6 AVX2 (14 Aug 2022)             www.cog-genomics.org/plink/2.0/
(C) 2005-2022 Shaun Purcell, Christopher Chang   GNU General Public License v3
Logging to /PROJECTES/HELIX_OMICS/analyses/GWAS_chemical_exposure_ZB/results/phthalates_mb/mecpp/mecpp.log.
Options in effect:
  --bfile /PROJECTES/HELIX_OMICS/data_final/gwas/child/8y/GSA_QC3.HRCimp_20210615/HELIX.impQC.rs.05.EUR
  --covar /PROJECTES/HELIX_OMICS/analyses/GWAS_chemical_exposure_ZB/db/HELIX_phtalates_cov_plink.txt
  --covar-name PC1, PC2, PC3, PC4, PC5, PC6, PC7, PC8, PC9, PC10, e3_sex, hs_child_age_days_None
  --covar-variance-standardize PC1, PC2, PC3, PC4, PC5, PC6, PC7, PC8, PC9, PC10, hs_child_age_days_None
  --glm
  --no-sex
  --out /PROJECTES/HELIX_OMICS/analyses/GWAS_chemical_exposure_ZB/results/phthalates_mb/mecpp/mecpp
  --pheno /PROJECTES/HELIX_OMICS/analyses/GWAS_chemical_exposure_ZB/db/HELIX_phtalates_cov_plink.txt
  --pheno-name hs_mecpp_cadj_Log2

Start time: Mon May 29 22:57:15 2023
515269 MiB RAM detected; reserving 257634 MiB for main workspace.
Using up to 72 threads (change this with --threads).
1155 samples (0 females, 0 males, 1155 ambiguous; 1155 founders) loaded from
/PROJECTES/HELIX_OMICS/data_final/gwas/child/8y/GSA_QC3.HRCimp_20210615/HELIX.impQC.rs.05.EUR.fam.
4614947 variants loaded from
/PROJECTES/HELIX_OMICS/data_final/gwas/child/8y/GSA_QC3.HRCimp_20210615/HELIX.impQC.rs.05.EUR.bim.
1 quantitative phenotype loaded (1044 values).
12 covariates loaded from /PROJECTES/HELIX_OMICS/analyses/GWAS_chemical_exposure_ZB/db/HELIX_phtalates_cov_plink.txt.
--covar-variance-standardize: 1 covariate transformed.
Calculating allele frequencies... done.
--glm linear regression on phenotype 'hs_mecpp_cadj_Log2': 8%...

When I read the results in R, I get the following table:

#CHROM    POS           ID REF ALT A1          TEST OBS_CT       BETA
1:      1 752721 1:752721:A:G   G   A  A           ADD    797  0.0259112
2:      1 752721 1:752721:A:G   G   A  A e3_sex=female    797 -0.0352766
3:      1 752721 1:752721:A:G   G   A  A           PC1    797  4.1562400
4:      1 752721 1:752721:A:G   G   A  A           PC2    797 11.8837000
5:      1 752721 1:752721:A:G   G   A  A           PC3    797  0.3141430
6:      1 752721 1:752721:A:G   G   A  A           PC4    797  2.8399700

I would like to know why OBS_CT (797) is different from the initial sample size (1044). I have checked and I do not have any missing values in the covariates.

I have read this explanation from PLINK but I do not understand it: "Finally, if PLINK 2 determines that any samples and covariates are irrelevant to all regressions (e.g. a covariate could be zero-valued for all but one sample), they are removed before any variants are processed. You can use the 'pheno-ids' modifier to make PLINK 2 report the remaining samples to (per-phenotype) .id files. (When the sample set changes on chrX or chrY, .x.id and/or .y.id files are also written.)"

Thank you in advance,

Mariona

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[Mariona Bustamante]

Hi

I think I have found the problem. The database contained many variables and one of them had a level with a "-". When I have eliminated this variable from the database (I did not use it for the analyses) and also changed --linear for --glm, it has worked. Not I got the 1044 in the OBS_CT.

Regards,

Mariona