Provided by: probabel_0.4.2-2_amd64
NAME
pacoxph - Perform Genome-Wide Association Analysis using a linear model
SYNOPSIS
pacoxph [ command-line options ]
DESCRIPTION
pacoxph 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 2). -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). --help Print help.
SEE ALSO
palinear(1), palogist(1)
BUGS
The bugtracker is located at https://r-forge.r-project.org/tracker/?group_id=505
AUTHORS
Lennart C. Karssen