pacoxph(1)

📦 version 0.5.0, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu resolute, ubuntu stonking

✨ pacoxph(1) — the GenABEL/ProbABEL era 💖

okay bestie so this is pacoxph, and it lives in the General Commands Manual, section 1. she's giving genome-wide association analysis with Cox' Proportional hazards model, and she is so good at it. let's get into it 🦋

🌸 NAME 🌸

pacoxph — run a Genome-Wide Association Analysis using Cox' Proportional hazards model. periodt. 💅

✨ SYNOPSIS ✨

pacoxph [ command-line options ]

that's it. that's the whole vibe. you just hand her options and she goes 🫶

💖 DESCRIPTION 💖

so like, pacoxph runs a linear regression on large imputed data sets, and she does it in an efficient way. that's the whole point. big data, no drama, no waiting around. iconic behaviour honestly 👑

🎀 Options 🎀

💅 Required command line options 💅

these ones are not optional bestie. she NEEDS them. no cap.

  • -p, --pheno FILE — read the phenotype data from FILE. this is the whole reason we're here, okay?
  • -i, --info FILE — read the SNP information from FILE, like an MLINFO file. SNP lore unlocked 🔍
  • -d, --dose FILE — the SNP predictor file name, so like MLDOSE or MLPROB. this is where the predictor data lives.

🌈 Optional command line options 🌈

these are the lil extras. add them if you want, skip them if you don't, she's chill like that.

  • -m, --map FILE — map file name. it holds the base pair positions for every SNP. lowkey essential for figuring out where things actually are 🗺️
  • -n, --nids NUMBER — how many people you're analysing. the headcount bestie.
  • -c, --chrom FILE — the chromosome, and yes this gets passed to the output. she's just being transparent 💁
  • -o, --out FILE — output file name. the default is regression.out.txt if you don't say anything, and honestly that's fine too.
  • -s, --skipd NUMBER — how many columns to skip in the predictor (dose/prob) file. default is 2. she's skipping past them like they're an ex in the hallway 🙈
  • -t, --ntraits NUMBER — how many traits are being analysed. default is 2.
  • -g, --ngpreds NUMBER — how many predictor columns there are per marker. default is 1 which means MLDOSE; otherwise use 2 for MLPROB. pick your fighter.
  • -a, --separat CHAR — use character CHAR to separate the fields in the output file(s). default is a space. cute and simple ✨
  • -r, --score — use the score test. that's it, that's the whole option.
  • -e, --no-head — do NOT report the header line in the output. she's shy, no header, no problem.
  • -f --flipmaf — flip the reference and effect allele according to Minor Allele Frequency (MAF), so that the minor allele becomes the effect/predictor allele. if you set this option, ProbABEL checks for each genetic variant whether the Freq1 column in the info file (see the --info option) is > 0.5, and if it is, she flips the probabilities/dosage of that variant so that A1 and A2 get interchanged. this will add a column called AllelesFlipped to the output file(s), and it tells you whether the alleles were flipped (1) or not (0). so you always know what happened, no mystery, we love accountability 🫶
  • -l --allcov — report estimates for ALL covariates. careful bestie — that's large outputs! (their words, not mine, and they put an exclamation mark on it so you KNOW it's serious 😭)
  • -b, --interaction NUMBER — which covariate to use for interaction with the SNP analysis. default is no interaction, 0. NUMBER is the column number of the covariate. so if you wanna be messy and interactive, this is your girl.
  • --help — print help. the classic. when in doubt, ask for help 💖

🦋 SEE ALSO 🦋

probabel(1), palinear(1), palogist(1)

her friends!! go say hi to them too, they're all part of the same squad 👑✨

💀 BUGS 💀

found something cursed? the bugtracker lives at:

https://github.com/GenABEL-Project/ProbABEL/issues

go report it there, don't suffer in silence bestie, that's what the issue tracker is for 🙈

🌟 AUTHORS 🌟

Lennart C. Karssen

we stan a legend 💜

okay that's the whole page, you're officially a pacoxph expert now. go run your GWAS, drink some water, and remember: minor allele is the effect allele when you flip that MAF. slay 🌈

💖 ProbABEL 0.5.0 — dated 4 May 2016 — that's the version and the date, and that's the sign-off, bye bestie!! 💖

📦 where this page comes from