debian/0000755000000000000000000000000012270514357007174 5ustar debian/upstream0000644000000000000000000000110312210410440010730 0ustar Contact: Richard Mott Homepage: http://www.well.ox.ac.uk/happy/happyR Name: happy.hbrem Reference: author: Mott, Richard and Talbot, Christopher J. and Turri, Maria G. and Collins, Allan C. and Flint, Jonathan title: A method for fine mapping quantitative trait loci in outbred animal stocks journal: Proc. Natl. Acad. Sci. USA volume: 97 number: 23 pages: 12649-12654 year: 2000 PMID: 11050180 DOI: 10.1073/pnas.230304397 URL: http://www.pnas.org/content/97/23/12649.abstract eprint: http://www.pnas.org/content/97/23/12649.full.pdf+html debian/patches/0000755000000000000000000000000012270514357010623 5ustar debian/patches/series0000644000000000000000000000002412270477413012035 0ustar happyMatrices.patch debian/patches/happyMatrices.patch0000644000000000000000000000133012210410440014430 0ustar Index: r-other-mott-happy-2.3/R/happy.R =================================================================== --- r-other-mott-happy-2.3.orig/R/happy.R +++ r-other-mott-happy-2.3/R/happy.R @@ -91,10 +91,12 @@ for( m in h$markers) { add <- hdesign( h, m, model='additive' ) full <- hdesign( h, m, model='full' ) - if ( h$use.pedigrees || h$phase.known ) + if ( (!is.null(h$use.pedigrees)&&h$use.pedigrees) || (!is.null(h$phase.known)&&h$phase.known) ) { full.asymmetric <- hdesign( h, m, model="full.asymmetric") - else + } + else { full.asymmetric <- NULL + } id <- m matrices[[m]] <- list( id=id, additive=add, full=full, full.asymmetric=full.asymmetric ) } debian/compat0000644000000000000000000000000212210410440010350 0ustar 9 debian/README.test0000644000000000000000000000043411704030455011024 0ustar Notes on how this package can be tested. ──────────────────────────────────────── This package can be tested by loading it into R with the command ‘library(happy)’ in order to confirm its integrity. debian/source/0000755000000000000000000000000012270514357010474 5ustar debian/source/format0000644000000000000000000000001411526060402011670 0ustar 3.0 (quilt) debian/README.Debian0000644000000000000000000000562611704030455011237 0ustar GNU R package for fine-mapping complex diseases Most phenotypes of medical importance can be measured quantitatively, and in many cases the genetic contribution is substantial, accounting for 40% or more of the phenotypic variance. Considerable efforts have been made to isolate the genes responsible for quantitative genetic variation in human populations, but with little success, mostly because genetic loci contributing to quantitative traits (quantitative trait loci, QTL) have only a small effect on the phenotype. Association studies have been proposed as the most appropriate method for finding the genes that influence complex traits. However, family-based studies may not provide the resolution needed for positional cloning, unless they are very large, while environmental or genetic differences between cases and controls may confound population-based association studies. . These difficulties have led to the study of animal models of human traits. Studies using experimental crosses between inbred animal strains have been successful in mapping QTLs with effects on a number of different phenotypes, including behaviour, but attempts to fine-map QTLs in animals have often foundered on the discovery that a single QTL of large effect was in fact due to multiple loci of small effect positioned within the same chromosomal region. A further potential difficulty with detecting QTLs between inbred crosses is the significant reduction in genetic heterogeneity compared to the total genetic variation present in animal populations: a QTL segregating in the wild need not be present in the experimental cross. . The idea behind this package is that when multiple strains of animals that differ in their susceptibility to multiple diseases are bread over multiple generations, then one can analyse the contribution that a particular genetic locus has to each of those diseases. While in the past this approach has been performed for one disease at a time, this tool extends the statistics for allowing multiple crosses and thus save animal lifes. A larger stock of animals with more generations to keep them will further help producing larger numbers of observable cross-over events and thus help increasing the resolution of the mapping. . Happy is an R interface into the HAPPY C package for fine-mapping Quantitative Trait Loci (QTL) in Heterogenous Stocks (HS). An HS is an advanced intercross between (usually eight) founder inbred strains of mice. HS are suitable for fine-mapping QTL. It uses a multipoint analysis which offers significant improvements in statistical power to detect QTLs over that achieved by single-marker association. . The happy package is an extension of the original C program happy; it uses the C code to compute the probability of descent from each of the founders, at each locus position, but the happy packager allows a much richer range of models to be fit to the data. debian/lintian-overrides0000644000000000000000000000014211704030455012543 0ustar # Usage of cdbs is hidden in r-cran.mk r-other-mott-happy source: unused-build-dependency-on-cdbs debian/copyright0000644000000000000000000000201512210410440011103 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Source: http://www.well.ox.ac.uk/happy/happy.hbrem_2.3.tar.gz Files: * Copyright: © Richard Mott License: GPL-2+ This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. . This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. . You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. Comment: On a Debian GNU/Linux system, the GPL license version 2 is included in the file /usr/share/common-licenses/GPL-2. debian/rules0000755000000000000000000000055512263773773010274 0ustar #!/usr/bin/make -f debRreposname := other-mott include /usr/share/R/debian/r-cran.mk # Remove once upstream adds a NAMESPACE file pre-build:: [ -f NAMESPACE ] || echo 'exportPattern("^[[:alpha:]]+")' > NAMESPACE override_dh_strip: dh_strip -Pr-other-mott-happy.hbrem --dbg-package=r-other-mott-happy.hbrem-dbg override_dh_clean: $(RM) NAMESPACE dh_clean debian/watch0000644000000000000000000000011711526060641010217 0ustar version=3 http://www.well.ox.ac.uk/happy/happyR.shtml happy.*_([\d\.]+).tar.gz debian/control0000644000000000000000000000466512270513440010602 0ustar Source: r-other-mott-happy Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller , Andreas Tille Section: gnu-r Priority: optional Build-Depends: debhelper (>= 9), cdbs, r-base-dev (>= 2.12), r-cran-g.data, r-cran-multicore, r-cran-mass Standards-Version: 3.9.5 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/R/r-other-mott-happy/trunk/ Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/R/r-other-mott-happy/trunk/ Homepage: http://www.well.ox.ac.uk/happy/happyR.shtml Package: r-other-mott-happy.hbrem Architecture: any Depends: ${shlibs:Depends}, ${R:Depends}, ${misc:Depends}, r-cran-g.data, r-cran-mass Recommends: r-cran-vr, r-cran-multicore Provides: r-other-mott-happy Conflicts: r-other-mott-happy, r-other-mott-happy.hbrem-dbg (<< ${binary:Version}) Replaces: r-other-mott-happy Description: GNU R package for fine-mapping complex diseases Happy is an R interface into the HAPPY C package for fine-mapping Quantitative Trait Loci (QTL) in Heterogenous Stocks (HS). An HS is an advanced intercross between (usually eight) founder inbred strains of mice. HS are suitable for fine-mapping QTL. It uses a multipoint analysis which offers significant improvements in statistical power to detect QTLs over that achieved by single-marker association. . The happy package is an extension of the original C program happy; it uses the C code to compute the probability of descent from each of the founders, at each locus position, but the happy packager allows a much richer range of models to be fit to the data. . Read /usr/share/doc/r-other-mott-happy/README.Debian for a more detailed explanation. Package: r-other-mott-happy.hbrem-dbg Architecture: any Section: debug Depends: ${misc:Depends}, r-other-mott-happy.hbrem (= ${binary:Version}) Description: Debug information for Happy R package native library The documentation of Happy is fairly complete, but the runtime itself does not inform as verbosely as users would like it on errors in configuration files. This debug package may complement nicely the on or other missing check on data integrity. . With this package installed, a debugger like 'gdb' indicates the position in the C implementation of R routines that spawned an error. debian/changelog0000644000000000000000000000715512270514253011051 0ustar r-other-mott-happy (2.4-1) unstable; urgency=low * New upstream version (Closes: #709190). * Revived the debug package. -- Steffen Moeller Fri, 24 Jan 2014 15:48:04 +0100 r-other-mott-happy (2.3-1) unstable; urgency=low * Team upload. [ Charles Plessy ] * New upstream version, renaming happy to happy.hbrem. * Simplified debian/rules following changes in r-base-dev 2.14.2~20120222-1 * Echo a dummy NAMESPACE file (Closes: #709190). * Use Debhelper 9. * Refreshed quilt patches. * Added Debhelper's misc:Depends substitution variable. * Normalised VCS URLs. * Normalised debian/control with config-model-edit. * Converted Debian copyright file to machine-readable format. * Conforms to Debian Policy version 3.9.4. * renamed debian/upstream-metadata.yaml to debian/upstream. [ Andreas Tille ] * debian/upstream: Fixed spelling of journal field -- Charles Plessy Sun, 30 Jun 2013 11:25:27 +0900 r-other-mott-happy (2.1-7) unstable; urgency=low * debian/control: Somehow missed dependencies from 2.1-5 - added again * Added debian/README.test -- Andreas Tille Sat, 17 Dec 2011 20:03:35 +0100 r-other-mott-happy (2.1-6) unstable; urgency=low [ Steffen Möller ] * debian/control: - Build-Depends: r-cran-multicore - Removed Recommends: r-cran-vr, r-cran-multicore * Source Format 3.0 (quilt) * debian/README.source (no need to tell what pacth is applied or not) * Debhelper 8 (control+compat) * debian/control: - Standards-Version: 3.9.2 (no changes needed) - Fixed Vcs fields - Versioned Build-Depends r-base-dev (>= 2.12) - Use Depends: ${R:Depends} as in all other R packages of Debian Med - Moved large parts of the long description to README.Debian Closes: #622295 * debian/rules: - Usual rules script of Debian Med team for R packages - Work around bug #652456 and call private copy of r-cran.mk to enable using source format 3.0 * debian/r-cran_without_simple-patchsys.mk --> This should be removed once #652456 is solved and a versioned Build-Depends should be used -- Andreas Tille Sat, 17 Dec 2011 13:05:47 +0100 r-other-mott-happy (2.1-5) unstable; urgency=low [Charles Plessy] * Documented information in ‘debian/upstream-metadata.yaml’. * Removed mention of the bibliographic reference in ‘debian/control’. [Andreas Tille] * debian/control: - Build-Depends r-base-dev (>= 2.10), Depends r-core (>= 2.10) and rebuild on current Squeeze system Closes: #611008 - Added myself to uploaders - Standards-Version: 3.9.1 (no changes needed) - Fixed name of Debian Med team - Debhelper 7 - Replaced (Build-)Depends r-cran-vr by r-cran-mass - Recommends: r-cran-vr, r-cran-multicore * Added watch file -- Andreas Tille Tue, 25 Jan 2011 08:17:57 +0100 r-other-mott-happy (2.1-4) unstable; urgency=low * Fixed build dependency on MASS library (packaged as r-cran-vr) (Closes: #544836). -- Steffen Moeller Thu, 03 Sep 2009 12:57:03 +0200 r-other-mott-happy (2.1-3) unstable; urgency=low * Corrected for architecture all -> any (Closes: #530007) -- Steffen Moeller Tue, 18 Aug 2009 17:13:41 +0200 r-other-mott-happy (2.1-2) UNRELEASED; urgency=low * Added patch for not using SET_VECTOR_ELT on strings -- Steffen Moeller Thu, 11 Jun 2009 18:28:33 +0200 r-other-mott-happy (2.1-1) UNRELEASED; urgency=low * Initial release. -- Steffen Moeller Fri, 22 May 2009 21:31:12 +0200