Plink-association test

Question

[Viktor Messi]

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!

[Nicolas Rosewick]

could you add your code please ?

[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