Is paxoxph function suitable for small dataset?

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shirleydaidai
Posts: 4
Joined: Tue Feb 14, 2017 7:00 am

Is paxoxph function suitable for small dataset?

Postby shirleydaidai » Fri Apr 20, 2018 6:58 am

Hello,
I was trying to run pacoxph for a small dataset (e.g. N=30). But all the results were "nan".

my code,

Code: Select all

for i in {1..22};do  /media/epiroot/_1/home/Dai/ProbABEL-0.5.0/bin/pacoxph  -p pheno.txt -d ../chr${i}/chr${i}_out.dose.fvi -i chr${i}.merge2.info --out coxres_chr${i}  --map chr${i}.map --chrom ${i}  --flipmaf  ; done


the output like this,

Code: Select all

name A1 A2 Freq1 MAF Quality Rsq n Mean_predictor_allele chrom position allelesFlipped beta_SNP_addA1 sebeta_SNP_addA1 chi2_SNP_add
rs149201999 C T 0.069 0.069 0.895 0.323 30 0.0393 22 16050408 0 nan nan nan
rs146752890 G C 0.127 0.127 0.821 0.337 30 0.0893167 22 16050612 0 nan nan nan
rs139377059 T C 0.065 0.065 0.904 0.345 30 0.03535 22 16050678 0 nan nan nan
rs6518357 A C 0.081 0.081 0.88 0.338 30 0.0599333 22 16051107 0 nan nan nan
rs62224609 C T 0.096 0.096 0.857 0.301 30 0.147767 22 16051249 0 nan nan nan
rs79725552 C T 0.085 0.085 0.875 0.342 30 0.0607 22 16051480 0 nan nan nan
rs2843213 T C 0.073 0.073 0.894 0.355 30 0.0510333 22 16051882 0 nan nan nan
rs2843217 C T 0.063 0.063 0.902 0.324 30 0.0488833 22 16052656 0 nan nan nan
rs2105538 A T 0.08 0.08 0.885 0.359 30 0.0565 22 16052838 0 nan nan nan
rs147891127 T G 0.075 0.075 0.896 0.374 30 0.0507 22 16053197 0 nan nan nan
rs141087528 T G 0.076 0.076 0.895 0.375 30 0.0509 22 16053435 0 nan nan nan
rs142325435 G A 0.076 0.076 0.897 0.391 30 0.0493667 22 16053509 0 nan nan nan


Are these "nan" due to the small sample size?

Thanks

Shirley

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