palogist(1)

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

✨ NAME ✨

palogist — bestie, this one does a Genome-Wide Association Analysis using a logistic model. 💖

🦋 SYNOPSIS 🦋

palogist [ command-line options ]

🌸 DESCRIPTION 🌸

So palogist runs a linear regression on large imputed data sets, and it does it in a genuinely efficient way. That's the whole vibe. Slay. 💅

👑 Options 👑

💖 Required command line options 💖

These ones? Not optional, bestie. You NEED them.

  • -p, --pheno FILE — Read the phenotype data from FILE.
  • -i, --info FILE — Read the SNP information from FILE (think an MLINFO file, iykyk).
  • -d, --dose FILE — The SNP predictor file name (like MLDOSE or MLPROB).

🎀 Optional command line options 🎀

These are the extras — take 'em or leave 'em, no pressure.

  • -m, --map FILE — Map file name, which holds the base pair positions for each SNP.
  • -n, --nids NUMBER — How many people to analyse.
  • -c, --chrom FILE — Chromosome (this gets passed through to the output).
  • -o, --out FILE — Output file name. The default is regression.out.txt.
  • -s, --skipd NUMBER — How many columns to skip in the predictor (dose/prob) file. Default is 2.
  • -t, --ntraits NUMBER — How many traits get analysed. Default is 1.
  • -g, --ngpreds NUMBER — How many predictor columns there are per marker. Default is 1 = MLDOSE; otherwise use 2 for MLPROB.
  • -a, --separat CHAR — Use character CHAR to separate the fields in the output file(s). Default is a space.
  • -r, --score — Use the score test.
  • -e, --no-head — Do not report the header line in the output. 🙈
  • -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 will check for each genetic variant whether the Freq1 column in the info file (peep the --info option) is > 0.5, and if it is, it'll flip that variant's probabilities/dosage so that A1 and A2 get interchanged. Heads up: this adds a column called AllelesFlipped to the output file(s), showing whether the alleles were flipped (1) or not (0). 🧚
  • -l --allcov — Report estimates for all covariates. (Large outputs! Like, huge. Be warned. 😭)
  • -b, --interaction NUMBER — Which covariate to use for interaction with the SNP analysis. Default is no interaction, 0. NUMBER is the column number of that covariate.
  • -v, --mmscore FILE — Score test in samples of related individuals. The FILE argument is the name of a file containing the inverse correlation matrix.
⚠️ NOTE THAT THIS FEATURE IS STILL EXPERIMENTAL! ⚠️
  • -u, --robust — Report robust standard errors (a.k.a. sandwich, a.k.a. Hubert-White). 💪
  • --help — Print help.

🌈 SEE ALSO 🌈

probabel(1), palinear(1), pacoxph(1)

💀 BUGS 💀

Found something cursed? The bugtracker lives at:

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

⭐ AUTHORS ⭐

Lennart C. Karssen — the icon, the moment, the legend. 👑

Okay bestie, that's the whole page — this is ProbABEL 0.5.0, dated 4 May 2016, and it's palogist(1) in the General Commands Manual. Go run some GWAS and be the main character. Periodt. 🫶✨

📦 where this page comes from