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Plink-association test

Hi,

I have been doing case control association test in plink. I have included sex and ethnic covar files, but is it normal for the results on summary, mperm and indiv to be the same with and without these covariates?

Thank you!

association plink case-control covar
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written by Viktor Messi • Viktor Messi

Hi, thank you for replying,

Here you go,

plink1 --noweb --map cohort_cleaned2.cnv.map --fam cohort_cleaned2.fam --cnv-list cohort_cleaned2.plink --pheno pheno_casecontrol_split.txt --adjust --logistic --covar cohort_cleaned2_covarethnic.cov --mperm 100000 --cnv-overlap 0.50 --cnv-exclude crm_imm_tlm_region_hg19_plink.txt --out cohort_cleaned2_cc_covarethnic

The terminal shows

Options in effect:

    --noweb
    --map cohort_cleaned2.cnv.map
    --fam cohort_cleaned2.fam
    --cnv-list cohort_cleaned2.plink
    --pheno pheno_casecontrol_split.txt
    --adjust
    --logistic
    --covar cohort_cleaned2_covarethnic.cov
    --mperm 100000
    --cnv-overlap 0.50
    --cnv-exclude crm_imm_tlm_region_hg19_plink.txt
    --out cohort_cleaned2_cc_covarethnic

Reading marker information from [ cohort_cleaned2.cnv.map ] 487 (of 487) markers to be included from [ cohort_cleaned2.cnv.map ] Reading individual information from [ cohort_cleaned2.fam ] Reading pedigree information from [ cohort_cleaned2.fam ] 217 individuals read from [ cohort_cleaned2.fam ] 213 individuals with nonmissing phenotypes Assuming a disease phenotype (1=unaff, 2=aff, 0=miss) Missing phenotype value is also -9 40 cases, 173 controls and 4 missing 59 males, 158 females, and 0 of unspecified sex Reading alternate phenotype from [ pheno_casecontrol_split.txt ] 215 individuals with non-missing alternate phenotype Assuming a disease phenotype (1=unaff, 2=aff, 0=miss) Missing phenotype value is also -9 41 cases, 174 controls and 2 missing 2 individuals removed because of missing phenotypes Reading 1 covariates from [ cohort_cleaned2_covarethnic.cov ] with nonmissing values for 215 individuals Reading CNV intersection list from [ crm_imm_tlm_region_hg19_plink.txt ] Read 51 ranges to exclude from CNV list Reading segment list (CNVs) from [ cohort_cleaned2.plink ] 625 mapped to a person, of which 625 passed filters 625 kept after excluding specific regions 625 of 786 mapped as valid segments

*CopyN Case/Control 0 34 / 120 1 8 / 37 3 72 / 352 4 0 / 2

Writing per-individual summary to [ cohort_cleaned2_cc_covarethnic.cnv.indiv ] Writing positional summary to [ cohort_cleaned2_cc_covarethnic.cnv.summary ] 41 affected individuals out of 215 in total Set to permute within 1 cluster(s) maxT permutation: 100000 of 100000 Writing permuted results for segment test to [ cohort_cleaned2_cc_covarethnic.cnv.summary.mperm ]

Analysis finished: Wed Apr 5 08:57:06 2023

Thank you

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written by Viktor Messi • Viktor Messi

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