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 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 correlation matrix. NOTE THAT THIS FEATURE IS STILL EXPERIMENTAL!

--robust

Report robust (a.k.a. sandwich, a.k.a. Hubert-White) standard errors.

--help

Print help.

AUTHORS

Lennart C. Karssen