Plink Alternative Phenotype File Columns not being Read

Plink Alternative Phenotype File Columns not being Read

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Hi, I have a plink alternative phenotype file with the following format:

FID IID Phenotype

1 2 1

1 3 0

etc.

As outlined in the plink documentation.

zzz.bwh.harvard.edu/plink/data.shtml#pheno

However, when I run the following command :

plink –bfile ../Plink_Files/plink –logistic –adjust –pheno ../Pheno_Files/pheno.txt –all-pheno –covar ../Cov_Files/pheno.txt –covar-number 2-4 –allow-no-sex –out Results/pheno

I get the following error message:

4768 people (0 males, 0 females, 4768 ambiguous) loaded from .fam.
Ambiguous sex IDs written to Results/Fibroids.nosex .
397 phenotype values present after –pheno.
Using 1 thread (no multithreaded calculations invoked).
–covar: 3 out of 11 covariates loaded.
1271 people were not seen in the covariate file.
Before main variant filters, 4768 founders and 0 nonfounders present.
Calculating allele frequencies… done.
Total genotyping rate is 0.943943.
94036 variants and 4768 people pass filters and QC.
Among remaining phenotypes, 0 are cases and 397 are controls. (4371 phenotypes
are missing.)
397 phenotype values present after –pheno.
Pheno has 0 cases, 397 controls, and 4371 missing phenotypes.

Which implies that the phenotype file is being read where the rows are phenotypes not the columns because it says the phenotypes are missing. I am not sure why that would be since the phenotype file matches the plink format that I found online. Any help in fixing this error would be greatly appreciated!


plink


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