NAME¶
smarteigenstrat - reduction of population bias for genetic analyses
SYNOPSIS¶
smarteigenstrat -i <genotypefile>
-a
<indivfile>
-b <snpfile>
-p <pcafile>
-o <outputfile>
-l <logfile>
-k
<numpca>
-q <qtlmode>
DESCRIPTION¶
The program
smarteigenstrat is part of EIGENSOFT.
The EIGENSOFT package combines functionality from the group's population
genetics methods (Patterson et al. 2006) and their EIGENSTRAT stratification
method (Price et al. 2006). The EIGENSTRAT method uses principal components
analysis to explicitly model ancestry differences between cases and controls
along continuous axes of variation; the resulting correction is specific to a
candidate marker's variation in frequency across ancestral populations,
minimizing spurious associations while maximizing power to detect true
associations. The EIGENSOFT package has a built-in plotting script and
supports multiple file formats and quantitative phenotypes.
OPTIONS¶
- -i
- genotype file (PED, PACKEDPED, EIGENSTRAT, ANCESTRYMAP or
PACKEDANCESTRYMAP format)-o output file (chisq)
- -l
- logfile (screen output,including error messages)
- -q
- YES for quantitative phenotype or NO otherwise
For quantitative phenotype, sixth column of .ped file or third column of
EIGENSTRAT .ind file should be real numbers. For non-quantitative phenotype,
sixth column of .ped or third column should be 'Case' or 'Control'
AUTHOR¶
This manpage was written by Andreas Tille for the Debian distribution and can be
used for any other usage of the program.