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[1] "Running with all traits in phenotype file: {working_dir}/phenofile.csv"
[1] "Validating phenotype data ..."
[1] "Number of columns in phenotype file: 6"
[1] "Phenotype file validated"
[1] "Validating trait of interest data ..."
[1] "Number of columns in trait of interest file:32"
[1] "Trait of interest file validated"
[1] "Loading phenotypes ..."
[1] "Loading trait of interest file ..."
[1] "Loading confounders from confounder file ..."
[1] "Number of rows in confounder data: 4998"
[1] "Number of INCOMPLETE rows removed from confounder data: 0"
[1] "Number of rows in confounder data: 4998"
[1] "Confounder columns:"
[1] "userID" "x3002_0_0" "x3001_0_0"
[1] "Phenotype file has 3490 rows with 3490 not NA for trait of interest (x5001_0_0)."
[1] "Phenotype and trait of interest data files merged, with 3490 examples"
[1] "Loading indicator fields from phenotypes file ..."
[1] "No required related variables."
[1] "LOADING DONE"
I'm facing this issue when I tried running PHESANT for my dataset (not UK Biobank). I've managed to create a smaller version of variable_list_file and datacoding file for my phenofile data. I have shared the screenshot of all my files to your mail. Kindly guide me with this issue.
The text was updated successfully, but these errors were encountered:
[1] "Running with all traits in phenotype file: {working_dir}/phenofile.csv"
[1] "Validating phenotype data ..."
[1] "Number of columns in phenotype file: 6"
[1] "Phenotype file validated"
[1] "Validating trait of interest data ..."
[1] "Number of columns in trait of interest file:32"
[1] "Trait of interest file validated"
[1] "Loading phenotypes ..."
[1] "Loading trait of interest file ..."
[1] "Loading confounders from confounder file ..."
[1] "Number of rows in confounder data: 4998"
[1] "Number of INCOMPLETE rows removed from confounder data: 0"
[1] "Number of rows in confounder data: 4998"
[1] "Confounder columns:"
[1] "userID" "x3002_0_0" "x3001_0_0"
[1] "Phenotype file has 3490 rows with 3490 not NA for trait of interest (x5001_0_0)."
[1] "Phenotype and trait of interest data files merged, with 3490 examples"
[1] "Loading indicator fields from phenotypes file ..."
[1] "No required related variables."
[1] "LOADING DONE"
I'm facing this issue when I tried running PHESANT for my dataset (not UK Biobank). I've managed to create a smaller version of variable_list_file and datacoding file for my phenofile data. I have shared the screenshot of all my files to your mail. Kindly guide me with this issue.
The text was updated successfully, but these errors were encountered: