| palogist(1) | General Commands Manual | palogist(1) |
NAME¶
palogist - Perform Genome-Wide Association Analysis using a logistic model
SYNOPSIS¶
palogist [ command-line options ]
DESCRIPTION¶
palogist runs a linear regression on large imputed data sets in an efficient way.
Options¶
Required command line options¶
- -p, --pheno FILE
- Read phenotype data from FILE
- -i, --info FILE
- Read SNP information from FILE (e.g. MLINFO file).
- -d, --dose FILE
- SNP predictor (e.g. MLDOSE/MLPROB) file name.
Optional command line options¶
- -m, --map FILE
- Map file name, containing base pair positions for each SNP.
- -n, --nids NUMBER
- Number of people to analyse.
- -c, --chrom FILE
- Chromosome (to be passed to output).
- -o, --out FILE
- Output file name (default is regression.out.txt ).
- -s, --skipd NUMBER
- How many columns to skip in predictor (dose/prob) file (default is 2).
- -t, --ntraits NUMBER
- How many traits are analysed (default is 1).
- -g, --ngpreds NUMBER
- How many predictor columns per marker (default 1 = MLDOSE; else use 2 for MLPROB).
- -a, --separat CHAR
- Use character CHAR to separate fields in the output file(s) (default is space).
- -r, --score
- Use the score test.
- -e, --no-head
- Do not report header line in the output.
- -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).
- -l --allcov
- Report estimates for all covariates (large outputs!).
- -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.
- -v, --mmscore FILE
- Score test in samples of related individuals. The FILE argument is the name of a file with the inverse correlation matrix. NOTE THAT THIS FEATURE IS STILL EXPERIMENTAL!
- -u, --robust
- Report robust (a.k.a. sandwich, a.k.a. Hubert-White) standard errors.
- --help
- Print help.
SEE ALSO¶
BUGS¶
The bugtracker is located at
https://github.com/GenABEL-Project/ProbABEL/issues
AUTHORS¶
Lennart C. Karssen
| 4 May 2016 | ProbABEL 0.5.0 |