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