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.