TRINCULO(1)

🌈 TRINCULO(1) — User Commands 🌈

hey bestie! welcome to TRINCULO(1), the User Commands manual page for trinculo! 💖 no cap, this is literally the toolkit to carry out genetic association for multi-category phenotypes, and we're about to go through it together. fr fr. 🧬✨

🎀 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 💅

okay so bestie, here's the full tea on every single flag. no skips, no cap. 💖

• MODE — Either multinom or ordinal for multinomial or ordinal logistic regression. it's giving choose-your-own-adventure, but make it stats. 💅
• --bfile FILE_PREFIX — Genotype input in binary plink format (FILE_PREFIX.bed, FILE_PREFIX.bim and FILE_PREFIX.fam). obsessed with a classic. 🧬
• --dosage FILE — Genotype input in dosage format. lowkey the alternative vibe. ✨
• --out PREFIX — The prefix used for output files [default is "trinculo"]. so if you don't say anything, it's literally just trinculo. periodt. 💖
• --pheno FILE — Phenotype input (same format as plink). main character energy. 👑
• --phenoname STRING — -The phenotype in the phenotype file to analyse. yes, exactly that one. 🎀
• --basepheno STRING — The reference category to use for the multinomial analysis [defaults to first category encountered]. it's giving baseline realness. 🌸
• --missingpheno STRING — The symbol to be use to indicate a missing phenotype in the phenotype file. (yes, "to be use" — we keep it exactly, bestie. 💀)
• --condition FILE — A file containing a list of SNPs (one per line) to conditon on (i.e. include as covariates). note the typo "conditon" — it's iconic, we keep it. 🦋
• --covar FILE — A file containing covariates to condition on (same format as plink). slay. 💅
• --normalize — Normalizes covariates to have a variance of 1 [off by default]. so it's off unless you say so. 🙈
• --priors FILE — A prior covariance matrix on effect sizes. it's giving Bayesian. 🔥
• --defaultpriors — Construct a prior matrix based on default values. easy mode. ✨
• --priorsigma VALUE — Set the prior variance on effect sizes within a disease [default is 0.04]. tiny but mighty. 🍓
• --priorcor VALUE — Set the prior correlation on effect sizes across diseases [default is 0]. no correlation by default, ngl. 💜
• --covarsigma VALUE — Prior on the covariate effect size [Default is 1]. one is the loneliest number. 😭
• --empiricalprior — -Calculate an empirical prior directly from the data. data said "I'll do it myself". 💅
• --noassoc — do not do any association testing, just infer the prior. it's giving minimal effort, but make it science. 🧚
• --select — -Do Bayesian model selection (i.e. calculate marginal likelihoods for each sharing model). model selection era. 👑
• --phenops — -Do a likelihood ratio test on each phenotype individually. one by one, bestie. 🌈
• --waldstats — -Calculate standard errors, Z scores and Wald p-values. stats on stats on stats. 🔥
• --errormat — -Output the variance-covariance matrix for the log odds ratio. matrix moment. 💖
• --fullmodel — -Output all parameter estimates and the full error matrix. the whole entire thing. periodt. 💅
• --threads n — Use up to n cores. parallelize, bestie. ⚡
• --precision DIGITS — Print output to DIGITS significant figures. precision is key. 🎯
• --fitIter NITER — Try up to NITER iterations when fitting models. keep trying. 💪
• --fitAbsTol ABSTOL — Terminate model fitting if results change by less than ABSTOL. absolute tolerance, no cap. ✨
• --fitRelTol RELTOL — Terminate model fitting if results change by less than (RELTOL x value). relative tolerance, slay. 💅
• --help — Prints this message. always here for you. 🫶

👑 AUTHOR 👑

this manpage was written by Pranav Ballaney for the Debian distribution, and it can be used for any other usage of the program. iconic behavior. 💖

and that's a wrap, bestie! 🫶 this has been trinculo 0.96, April 2020, TRINCULO(1). periodt. 💅✨