NAME

       probabel - Wrapper around the three ProbABEL binaries, simplifying their use

SYNOPSIS

       probabel CHROM-START CHROM-STOP METHOD COHORT MODEL PHENOTYPE [OTHER_OPTIONS]

DESCRIPTION

       probabel is a wrapper around the three ProbABEL binaries: palinear, palogist, and pacoxph.

       It  is designed to simplify runnig of a Genome-Wide Association Study (GWAS) by saving the
       user's precious time in two ways:

       1) it runs the regression analysis of all chromosomes from CHROM-START to CHROM-STOP.

       2) In contrast to the three binaries mentioned above, with probabel the user doesn't  need
       to  specify  the locations of the required genetic data files. Their location is centrally
       managed in a configuration file (/etc/probabel_config.cfg by default).

OPTIONS

   Required command line options
       CHROM-START
              Number of the chromosome to start the analysis at.

       CHROM-END
              Number of the chromosome to end the analysis at.

       Note that analysis of a single chromosome can be run by specifying  the  same  number  for
       CHROM-START  and  CHROM-STOP.  In  fact,  this  is  the way to run analysis for the X or Y
       chromosome

       METHOD Which regression method to use, can be one of linear, logistic, or coxph.

       COHORT The name of the cohort as defined in the /etc/probabel_config.cfg file.  Using  the
              cohort  identifier  from  the  config  file the three actual ProbABEL binaries know
              where to find the genotypic information  files  (dosage  files  and/or  probability
              files).

       MODEL  The  genetic  model  to  be  used.  Can be either --additive for the additive model
              (requires genotype data in dosage form), or --allmodels to run all genetic  models:
              additive, recessive, dominant, over-dominant and 2df.

       PHENOTYPE
              The name of the phenotype file, without its extension (which should be .PHE!).

   Other options
       Any options listed after the (mandatory) previous ones will be passed on to the underlying
       binary: palinear, palogist or pacoxph, depending on the METHOD.

       The most commonly used option is the -o option, followed by a file  name,  this  specifies
       the beginning of the file name for the output files.

   Additional options
       -h,  --help  Get  additional  help  on how to run probabel. In this case none of the other
       options needs to be specified.

EXAMPLES

       This runs a genome-wide association scan using linear regression and the additive  genetic
       model on cohort My_Large_Cohort for phenotype my_phenotype:

              probabel 1 22 linear "My_Large_Cohort" --additive my_phenotype

SEE ALSO

       palinear(1), palogist(1), pacoxph(1)

BUGS

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

AUTHORS

       Lennart C. Karssen