Content-type: text/html Man page of EMFBAT

EMFBAT

Section: USER COMMANDS (1)
Updated: June 15, 2008
Index Return to Main Contents
 

NAME

emfbat - Family Based Association Testing  

SYNOPSIS

emfbat [options] files  

DESCRIPTION

emfbat performs a Family Based Association Test robust to genotyping errors and missing genotypes. emfbat is part of the software library libfbat.  

ARGUMENTS

file.ped
Pedigree file, with on the first line the names of all markers, and on the remaining lines the pedigree ID, the father ID and mother ID (use 0 for founders or unknown parents), the sex (1=male, 2=female), the affection status (not used) and the alleles (space-delimited) for each marker (tab-delimited). All IDs and marker names are composed of strings of any characters whithout space or tab.
file.phe
Phenotype file, with on the first line the names of all traits, and on the remaining lines the pedigree ID, the individual ID and all the trait values (tab-delimited, a single hyphen (-) for missing traits).
 

OPTIONS

-x int, --xfunc int
Select the X function for int in 1==Additive, 2==Dominant, 3==Recessive 4==Genotype (Default: 1).
-n int, --multi int
Number of successive markers (Default: 1).
-a int, --nbal int
Number of alleles (Default: 2).
-c int, --nbchange int
Maximal number of genotype changes (Default: 1).
-f float, --offset float
FBAT offset (Default: 0.).
-r float, --emerror float
Initial genotyping error of EM (Default: 0.05).
-e int, --emnbiter int
Number of EM iterations (Default: 10).
-s string, --select string
Displays the statistics only for a selected marker or marker succession (use "-" between successive markers).
-g --general
Displays a general summary of each X function component.
--verbose
Verbose mode.
-v --version
Displays the version number and exit.
-h --help
Prints this help and exit.
 

AUTHORS

emfbat is developed by Vincent Miele <miele@biomserv.univ-lyon1.fr> under the terms of the GNU License, on the scientifical direction of Gregory Nuel <Gregory.Nuel@math-info.univ-paris5.fr>.  

SEE ALSO

More information on emfbat and libfbat is available at <http://pbil.univ-lyon1.fr>.

 

Index

NAME
SYNOPSIS
DESCRIPTION
ARGUMENTS
OPTIONS
AUTHORS
SEE ALSO
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Time: 13:14:27 GMT, June 23, 2008