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: ===================================== debian/manpages ===================================== @@ -0,0 +1 @@ +debian/*.1 ===================================== debian/trinculo.1 ===================================== @@ -0,0 +1,52 @@ +.\" 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 -- View it on GitLab: https://salsa.debian.org/med-team/trinculo/-/commit/b38e14a37fe023eb742207c64bc62cb948a75c3d You're receiving this email because of your account on salsa.debian.org.
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