.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.13.
.TH TRINCULO "1" "April 2020" "trinculo 0.96" "User Commands"
.SH NAME
trinculo \- toolkit to carry out genetic association for multi-category phenotypes
.SH DESCRIPTION
Running a multinomial logistic analysis
.SS "Usage:"
.TP
trinculo MODE
[\-\-bfile GENOTYPES_PREFIX | \fB\-\-dosage\fR GENOTYPES.DOSE ] [\-\-out OUTPUT_PREFIX] \fB\-\-pheno\fR PHENOTYPES.TXT \fB\-\-phenoname\fR PHENOTYPE [\-\-basepheno REF \fB\-\-missingpheno\fR MISSING ] [\-\-covar COVARIATES.TXT \fB\-\-normalize]\fR [\-\-condition SNPS.TXT] [\-\-priors PRIORS.TXT | \fB\-\-defaultprior\fR \fB\-\-priorsigma\fR PRIORVAR \fB\-\-priorcor\fR PRIORCOR \fB\-\-covarsigma\fR PRIORVAR | \fB\-\-empiricalprior\fR  ] [ \fB\-\-select\fR \fB\-\-phenops\fR \fB\-\-errormat\fR \fB\-\-fullmodel\fR \fB\-\-waldstats\fR ] [ \fB\-\-noassoc\fR ] [\-\-threads n] [ \fB\-\-precision\fR DIGITS ] [ \fB\-\-fitIter\fR NITER \fB\-\-fitAbsTol\fR ABSTOL \fB\-\-fitRelTol\fR RELTOL ] [\-\-help]
.SH OPTIONS
MODE    \- Either multinom or ordinal for multinomial or ordinal logistic regression
.PP
\fB\-\-bfile\fR FILE_PREFIX     \- Genotype input in binary plink format (FILE_PREFIX.bed, FILE_PREFIX.bim and FILE_PREFIX.fam)
\fB\-\-dosage\fR FILE   \- Genotype input in dosage format
\fB\-\-out\fR PREFIX    \- The prefix used for output files [default is "trinculo"]
.PP
\fB\-\-pheno\fR FILE    \- Phenotype input (same format as plink)\-\-phenoname STRING      \fB\-The\fR phenotype in the phenotype file to analyse
\fB\-\-basepheno\fR STRING      \- The reference category to use for the multinomial analysis [defaults to first category encountered]
\fB\-\-missingpheno\fR STRING   \- The symbol to be use to indicate a missing phenotype in the phenotype file
.PP
\fB\-\-condition\fR FILE        \- A file containing a list of SNPs (one per line) to conditon on (i.e. include as covariates)
.PP
\fB\-\-covar\fR FILE    \- A file containing covariates to condition on (same format as plink)
\fB\-\-normalize\fR     \- Normalizes covariates to have a variance of 1 [off by default]
.PP
\fB\-\-priors\fR FILE   \- A prior covariance matrix on effect sizes
\fB\-\-defaultpriors\fR \- Construct a prior matrix based on default values
\fB\-\-priorsigma\fR VALUE      \- Set the prior variance on effect sizes within a disease[default is 0.04]
\fB\-\-priorcor\fR VALUE        \- Set the prior correlation on effect sizes across diseases [default is 0]
\fB\-\-covarsigma\fR VALUE      \- Prior on the covariate effect size [Default is 1]
\fB\-\-empiricalprior\fR         \- Calculate an empirical prior directly from the data
\fB\-\-noassoc\fR       \fB\-do\fR not do any association testing, just infer the prior
.PP
\fB\-\-select\fR        \fB\-Do\fR Bayesian model selection (i.e. calculate marginal likelihoods for each sharing model)
\fB\-\-phenops\fR       \fB\-Do\fR a likelihood ratio test on each phenotype individually
\fB\-\-waldstats\fR     \fB\-Calculate\fR standard errors, Z scores and Wald p\-values
\fB\-\-errormat\fR      \fB\-Output\fR the variance\-covariance matrix for the log odds ratio
\fB\-\-fullmodel\fR     \fB\-Output\fR all parameter estimates and the full error matrix
.PP
\fB\-\-threads\fR n     Use up to n cores
.PP
\fB\-\-precision\fR DIGITS      Print output to DIGITS significant figures
.PP
\fB\-\-fitIter\fR NITER Try up to NITER iterations when fitting models
\fB\-\-fitAbsTol\fR ABSTOL      Terminate model fitting if results change by less than ABSTOL
\fB\-\-fitRelTol\fR RELTOL      Terminate model fitting if results change by less than (RELTOL x value)
.PP
\fB\-\-help\fR  \- Prints this message
.SH AUTHOR
 This manpage was written by Pranav Ballaney for the Debian distribution and
 can be used for any other usage of the program.