[med-svn] [Git][med-team/trinculo][master] Add manpage

[Pranav Ballaney]

Pranav Ballaney pushed to branch master at Debian Med / trinculo


Commits:
b38e14a3 by Pranav Ballaney at 2020-04-09T00:04:02+05:30
Add manpage

- - - - -


2 changed files:

- + debian/manpages
- + debian/trinculo.1


Changes:

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debian/manpages
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+debian/*.1


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debian/trinculo.1
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+.\" 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-catagory 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 catagory to use for the multinomial analysis [defaults to first catagory 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.



View it on GitLab: https://salsa.debian.org/med-team/trinculo/-/commit/b38e14a37fe023eb742207c64bc62cb948a75c3d

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