This is the command palogist that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
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 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.
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