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<h3>
Pranav Ballaney pushed to branch master
at <a href="https://salsa.debian.org/med-team/trinculo">Debian Med / trinculo</a>
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Commits:
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<strong><a href="https://salsa.debian.org/med-team/trinculo/-/commit/b38e14a37fe023eb742207c64bc62cb948a75c3d">b38e14a3</a></strong>
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<span>by Pranav Ballaney</span>
<i>at 2020-04-09T00:04:02+05:30</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add manpage
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<h4>2 changed files:</h4>
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debian/manpages
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debian/trinculo.1
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<h4>Changes:</h4>
<li id="68e0b13744e158347bfd74ebaaca667435f07d14">
<a href="https://salsa.debian.org/med-team/trinculo/-/commit/b38e14a37fe023eb742207c64bc62cb948a75c3d#68e0b13744e158347bfd74ebaaca667435f07d14"><strong>debian/manpages</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">debian/*.1</span></pre>
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<a href="https://salsa.debian.org/med-team/trinculo/-/commit/b38e14a37fe023eb742207c64bc62cb948a75c3d#034b9bb01282987fbf0fd8d02a1826edca4c556b"><strong>debian/trinculo.1</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.13.</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH TRINCULO "1" "April 2020" "trinculo 0.96" "User Commands"</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">.SH NAME</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">trinculo \- toolkit to carry out genetic association for multi-catagory phenotypes</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">.SH DESCRIPTION</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">Running a multinomial logistic analysis</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">.SS "Usage:"</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">trinculo MODE</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">[\-\-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]</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">.SH OPTIONS</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">MODE \- Either multinom or ordinal for multinomial or ordinal logistic regression</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">\fB\-\-bfile\fR FILE_PREFIX \- Genotype input in binary plink format (FILE_PREFIX.bed, FILE_PREFIX.bim and FILE_PREFIX.fam)</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">\fB\-\-dosage\fR FILE \- Genotype input in dosage format</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">\fB\-\-out\fR PREFIX \- The prefix used for output files [default is "trinculo"]</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">\fB\-\-pheno\fR FILE \- Phenotype input (same format as plink)\-\-phenoname STRING \fB\-The\fR phenotype in the phenotype file to analyse</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">\fB\-\-basepheno\fR STRING \- The reference catagory to use for the multinomial analysis [defaults to first catagory encountered]</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">\fB\-\-missingpheno\fR STRING \- The symbol to be use to indicate a missing phenotype in the phenotype file</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">\fB\-\-condition\fR FILE \- A file containing a list of SNPs (one per line) to conditon on (i.e. include as covariates)</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">\fB\-\-covar\fR FILE \- A file containing covariates to condition on (same format as plink)</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">\fB\-\-normalize\fR \- Normalizes covariates to have a variance of 1 [off by default]</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">\fB\-\-priors\fR FILE \- A prior covariance matrix on effect sizes</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">\fB\-\-defaultpriors\fR \- Construct a prior matrix based on default values</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">\fB\-\-priorsigma\fR VALUE \- Set the prior variance on effect sizes within a disease[default is 0.04]</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">\fB\-\-priorcor\fR VALUE \- Set the prior correlation on effect sizes across diseases [default is 0]</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">\fB\-\-covarsigma\fR VALUE \- Prior on the covariate effect size [Default is 1]</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">\fB\-\-empiricalprior\fR \- Calculate an empirical prior directly from the data</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">\fB\-\-noassoc\fR \fB\-do\fR not do any association testing, just infer the prior</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">\fB\-\-select\fR \fB\-Do\fR Bayesian model selection (i.e. calculate marginal likelihoods for each sharing model)</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">\fB\-\-phenops\fR \fB\-Do\fR a likelihood ratio test on each phenotype individually</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">\fB\-\-waldstats\fR \fB\-Calculate\fR standard errors, Z scores and Wald p\-values</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">\fB\-\-errormat\fR \fB\-Output\fR the variance\-covariance matrix for the log odds ratio</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">\fB\-\-fullmodel\fR \fB\-Output\fR all parameter estimates and the full error matrix</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">\fB\-\-threads\fR n Use up to n cores</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">\fB\-\-precision\fR DIGITS Print output to DIGITS significant figures</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">\fB\-\-fitIter\fR NITER Try up to NITER iterations when fitting models</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext">\fB\-\-fitAbsTol\fR ABSTOL Terminate model fitting if results change by less than ABSTOL</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">\fB\-\-fitRelTol\fR RELTOL Terminate model fitting if results change by less than (RELTOL x value)</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">\fB\-\-help\fR \- Prints this message</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext">.SH AUTHOR</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext"> This manpage was written by Pranav Ballaney for the Debian distribution and</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext"> can be used for any other usage of the program.</span></pre>
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