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palinear(1) General Commands Manual palinear(1)

NAME

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

SYNOPSIS

palinear [ command-line options ]

DESCRIPTION

palinear 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 of the variance-covariance matrix.
-u, --robust
Report robust (a.k.a. sandwich, a.k.a. Hubert-White) standard errors.
--help
Print help.

SEE ALSO

probabel(1), palogist(1), pacoxph(1)

BUGS

The bugtracker is located at
https://github.com/GenABEL-Project/ProbABEL/issues

AUTHORS

Lennart C. Karssen
4 May 2016 ProbABEL 0.5.0