NAME

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

DESCRIPTION

       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]

OPTIONS

       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

AUTHOR

        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)