trinculo - toolkit to carry out genetic association for multi-category phenotypes

        This manpage was written by Pranav Ballaney for the Debian distribution and
        can be used for any other usage of the program.

trinculo 0.96                                      April 2020                                        TRINCULO(1)

       Running a multinomial logistic analysis

   Usage:
       trinculo MODE
              [--bfile GENOTYPES_PREFIX | --dosage GENOTYPES.DOSE ] [--out OUTPUT_PREFIX] --pheno PHENOTYPES.TXT
              --phenoname   PHENOTYPE   [--basepheno   REF  --missingpheno  MISSING  ]  [--covar  COVARIATES.TXT
              --normalize] [--condition SNPS.TXT] [--priors PRIORS.TXT |  --defaultprior--priorsigma  PRIORVAR
              --priorcor  PRIORCOR  --covarsigma  PRIORVAR | --empiricalprior  ] [ --select--phenops--errormat--fullmodel--waldstats ] [ --noassoc ] [--threads n] [ --precision DIGITS  ]  [  --fitIter  NITER
              --fitAbsTol ABSTOL --fitRelTol RELTOL ] [--help]

       trinculo - toolkit to carry out genetic association for multi-category phenotypes

       MODE    - Either multinom or ordinal for multinomial or ordinal logistic regression

       --bfile  FILE_PREFIX      -  Genotype  input in binary plink format (FILE_PREFIX.bed, FILE_PREFIX.bim and
       FILE_PREFIX.fam) --dosage FILE   - Genotype input in dosage format --out PREFIX    - The prefix used  for
       output files [default is "trinculo"]

       --pheno  FILE     -  Phenotype  input (same format as plink)--phenoname STRING      -The phenotype in the
       phenotype file to analyse --basepheno STRING      - The reference category to  use  for  the  multinomial
       analysis  [defaults  to  first  category  encountered]  --missingpheno STRING   - The symbol to be use to
       indicate a missing phenotype in the phenotype file

       --condition FILE        - A file containing a list of SNPs (one per line) to conditon on (i.e. include as
       covariates)

       --covar FILE    - A file containing covariates to condition on (same format as plink)  --normalize      -
       Normalizes covariates to have a variance of 1 [off by default]

       --priors  FILE    -  A prior covariance matrix on effect sizes --defaultpriors - Construct a prior matrix
       based on default values --priorsigma VALUE      - Set  the  prior  variance  on  effect  sizes  within  a
       disease[default  is  0.04]  --priorcor  VALUE         -  Set the prior correlation on effect sizes across
       diseases [default is 0] --covarsigma VALUE      - Prior on the  covariate  effect  size  [Default  is  1]
       --empiricalprior         - Calculate an empirical prior directly from the data --noassoc-do not do
       any association testing, just infer the prior

       --select-Do Bayesian model selection (i.e. calculate marginal likelihoods for each sharing model)
       --phenops-Do  a  likelihood  ratio test on each phenotype individually --waldstats-Calculate
       standard errors, Z scores and Wald p-values --errormat-Output the  variance-covariance  matrix  for
       the log odds ratio --fullmodel-Output all parameter estimates and the full error matrix

       --threads n     Use up to n cores

       --precision DIGITS      Print output to DIGITS significant figures

       --fitIter  NITER  Try  up to NITER iterations when fitting models --fitAbsTol ABSTOL      Terminate model
       fitting if results change by less than ABSTOL --fitRelTol RELTOL      Terminate model fitting if  results
       change by less than (RELTOL x value)

       --help  - Prints this message