palinear(1)

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

💖 palinear(1) — the linear-model GWAS girlie 💖

okay so bestie, welcome to palinear, from the General Commands Manual section. she's giving "run a whole genome-wide association analysis and make it look easy" ✨

🌸 NAME 🌸

palinear — Perform Genome-Wide Association Analysis using a linear model 🧬

✨ SYNOPSIS ✨

palinear [ command-line options ]

that's it. that's the whole vibe. you hand her options, she hands you regression results 💅

🦋 DESCRIPTION 🦋

palinear runs a linear regression on large imputed data sets, and she does it in an efficient way. no cap. big data, tiny runtime, main character energy fr fr 🔥

🎀 Options 🎀

💜 Required command line options 💜

these ones? not optional. she needs them. periodt.

  • -p, --pheno FILE — Read phenotype data from FILE. like, the actual thing you're studying bestie, can't regress on nothing 🙈
  • -i, --info FILE — Read SNP information from FILE (e.g. MLINFO file). the SNP lore goes here 📋
  • -d, --dose FILE — SNP predictor (e.g. MLDOSE/MLPROB) file name. the actual dosage/probability data, the star of the show 👑

🌈 Optional command line options 🌈

these are the "if you want" girlies. she works without them, but they make her shine ✨

  • -m, --map FILE — Map file name, containing base pair positions for each SNP. where each SNP lives on the chromosome, geographically speaking 🗺️
  • -n, --nids NUMBER — Number of people to analyse. how many besties are in the study 🫶
  • -c, --chrom FILE — Chromosome (to be passed to output). she just forwards it straight to the output, no thoughts, head empty, iconic 💅
  • -o, --out FILE — Output file name (default is regression.out.txt). where the receipts go 🧾
  • -s, --skipd NUMBER — How many columns to skip in predictor (dose/prob) file (default is 2). skip past the boring leading columns like they're an ex 🚶‍♀️
  • -t, --ntraits NUMBER — How many traits are analysed (default is 1). multitasking queen 💅
  • -g, --ngpreds NUMBER — How many predictor columns per marker (default 1 = MLDOSE; else use 2 for MLPROB). one column of dosage or two of probability, pick your fighter 🥊
  • -a, --separat CHAR — Use character CHAR to separate fields in the output file(s) (default is space). choose your delimiter, customize your life 🎀
  • -r, --score — Use the score test. score test era ⭐
  • -e, --no-head — Do not report header line in the output. no header, we die like women (metaphorically, it's just a missing line) 💀
  • -f, --flipmaf — Flip reference and effect allele according to Minor Allele Frequency (MAF) such that the minor allele is the effect/predictor allele. If this option is set, ProbABEL will check for each genetic variant whether the Freq1 column in the info file (see the --info option) is > 0.5 and if so will flip the probabilities/dosage of that variant such that A1 and A2 are interchanged. This will add a column called AllelesFlipped to the output file(s), indicating whether the alleles were flipped (1) or not (0). okay this one is a whole paragraph but she's worth it — the minor allele takes the spotlight, and you get a whole AllelesFlipped column to prove it 🔄
  • -l, --allcov — Report estimates for all covariates (large outputs!). heads up bestie, this makes the output BIG — she literally put the exclamation mark in there herself 😭
  • -b, --interaction NUMBER — Which covariate to use for interaction with SNP analysis (default is no interaction, 0). NUMBER indicates the column number of the covariate. tell her which covariate wants to interact with the SNP, by column number 🤝
  • -v, --mmscore FILE — Score test in samples of related individuals. The FILE argument is the name of a file with the inverse of the variance-covariance matrix. related individuals? she's got a matrix for that (the inverse one, specifically) 🧮
  • -u, --robust — Report robust (a.k.a. sandwich, a.k.a. Hubert-White) standard errors. sandwich errors?? we love a well-fed standard error 🥪
  • --help — Print help. when in doubt, ask her directly 🫶

👀 SEE ALSO 👀

go hang out with her sisters:

💀 BUGS 💀

found a bug? do not suffer in silence. The bugtracker is located at:

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

go tell them, they'll fix it, slay 🐛🔨

👑 AUTHORS 👑

Lennart C. Karssen — thank you for your service, legend 🫡💖

and that's the whole page bestie!! this manual is from ProbABEL 0.5.0, dated 4 May 2016, and yeah she's a little vintage but she's still iconic and she still runs your GWAS ✨🧬💅 bye babes, go run some regressions 🌈💖

📦 where this page comes from