Bug#641724: RFP: eigensoft -- reduction of statistical effects by population co-inheritance
Package: wnpp
Severity: wishlist
* Package name : eigensoft
Version : 4.2
* URL : http://www.hsph.harvard.edu/faculty/alkes-price/software/
* License : non-free but redistributable
Programming Lang: C, Perl
Description : reduction of statistical effects by population co-inheritance
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.
The package is mostly ready at
http://anonscm.debian.org/viewvc/debian-med/trunk/packages/eigensoft/trunk/
of the Debian Med repository. It still has a series of lintian errors
W: eigensoft source: dbg-package-missing-depends eigensoft-dbg
W: eigensoft: new-package-should-close-itp-bug
W: eigensoft: wrong-bug-number-in-closes l3:#nnnn
E: eigensoft: helper-templates-in-copyright
E: eigensoft: helper-templates-in-copyright
E: eigensoft: helper-templates-in-copyright
W: eigensoft: copyright-has-url-from-dh_make-boilerplate
E: eigensoft: copyright-contains-dh_make-todo-boilerplate
W: eigensoft: binary-without-manpage usr/bin/baseprog
W: eigensoft: binary-without-manpage usr/bin/convertf
W: eigensoft: binary-without-manpage usr/bin/eigenstrat
W: eigensoft: binary-without-manpage usr/bin/eigenstrat.big.perl
W: eigensoft: binary-without-manpage usr/bin/eigenstratQTL
W: eigensoft: binary-without-manpage usr/bin/eigenstratQTL.big.perl
W: eigensoft: binary-without-manpage usr/bin/evec2pca.perl
W: eigensoft: binary-without-manpage usr/bin/fixgreen
W: eigensoft: binary-without-manpage usr/bin/gc.perl
W: eigensoft: binary-without-manpage usr/bin/mergeit
W: eigensoft: binary-without-manpage usr/bin/pca
W: eigensoft: binary-without-manpage usr/bin/pcatoy
W: eigensoft: binary-without-manpage usr/bin/ploteig
W: eigensoft: binary-without-manpage usr/bin/smarteigenstrat
W: eigensoft: binary-without-manpage usr/bin/smarteigenstrat.perl
W: eigensoft: binary-without-manpage usr/bin/smartpca
W: eigensoft: binary-without-manpage usr/bin/smartpca.perl
W: eigensoft: binary-without-manpage usr/bin/smartrel
W: eigensoft: binary-without-manpage usr/bin/twstats
W: eigensoft: unusual-interpreter usr/share/eigenstrat/POPGEN/HGDP.X.perl #!/usr/bin
W: eigensoft-dbg: new-package-should-close-itp-bug
W: eigensoft-dbg: wrong-bug-number-in-closes l3:#nnnn
E: eigensoft-dbg: helper-templates-in-copyright
E: eigensoft-dbg: helper-templates-in-copyright
E: eigensoft-dbg: helper-templates-in-copyright
W: eigensoft-dbg: copyright-has-url-from-dh_make-boilerplate
E: eigensoft-dbg: copyright-contains-dh_make-todo-boilerplate
and needs the OK by upstream, still.
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