Ubuntu Manpage: palinear - Perform Genome-Wide Association Analysis using a linear model

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 FILE
Character to separate fields (default is space).

-r, --score
Use the score test.

-e, --no-head
Do not report header line in the output.

-l --allcov
Report estimates for all covariates (large outputs!).

-b, --interaction
Which covariate to use for interaction with SNP analysis (default is no interaction, 0).

-k, --interaction_only
Like --interaction but without covariate acting in interaction with SNP (default is no
interaction, 0).

-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.

BUGS

       The bugtracker is located at
       https://r-forge.r-project.org/tracker/?group_id=505

AUTHORS