[med-svn] [r-cran-genabel.data] 03/05: New upstream version 1.0.0
Andreas Tille
tille at debian.org
Thu Oct 19 13:27:23 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository r-cran-genabel.data.
commit 491143a4812aa5aa486803dfcf6abe4733a7cb9c
Author: Andreas Tille <tille at debian.org>
Date: Thu Oct 19 15:23:41 2017 +0200
New upstream version 1.0.0
---
DESCRIPTION | 18 ++++++++++++++
MD5 | 12 +++++++++
NAMESPACE | 1 +
data/datalist | 6 +++++
data/ge03d2.RData | Bin 0 -> 886288 bytes
data/ge03d2.clean.RData | Bin 0 -> 727828 bytes
data/ge03d2c.RData | Bin 0 -> 237324 bytes
data/ge03d2ex.RData | Bin 0 -> 104860 bytes
data/ge03d2ex.clean.RData | Bin 0 -> 84032 bytes
data/srdta.RData | Bin 0 -> 364556 bytes
debian/README.source | 59 --------------------------------------------
debian/changelog | 5 ----
debian/compat | 1 -
debian/control | 27 --------------------
debian/copyright | 30 ----------------------
debian/rules | 3 ---
debian/source/format | 1 -
debian/watch | 2 --
man/GenABEL.data-package.Rd | 36 +++++++++++++++++++++++++++
man/ge03d2.Rd | 55 +++++++++++++++++++++++++++++++++++++++++
man/srdta.Rd | 42 +++++++++++++++++++++++++++++++
21 files changed, 170 insertions(+), 128 deletions(-)
diff --git a/DESCRIPTION b/DESCRIPTION
new file mode 100644
index 0000000..e9d5aa9
--- /dev/null
+++ b/DESCRIPTION
@@ -0,0 +1,18 @@
+Package: GenABEL.data
+Type: Package
+Title: Package contains data which is used by GenABEL example and test
+ functions
+Version: 1.0.0
+Date: 2013-12-09
+Author: Maksim Struchalin <m.v.struchalin at mail.ru> and GenABEL project developers <genabel.project at gmail.com>
+Maintainer: Maksim Struchalin <m.v.struchalin at mail.ru>
+Depends: R (>= 2.15.0)
+Description: GenABEL.data package consists of a data set used by GenABEL functions
+License: GPL (>= 2)
+URL: http://www.genabel.org, http://forum.genabel.org,
+ http://genabel.r-forge.r-project.org/
+BugReports: http://r-forge.r-project.org/tracker/?group_id=505
+Packaged: 2013-12-26 07:27:47 UTC; maksim
+NeedsCompilation: no
+Repository: CRAN
+Date/Publication: 2013-12-27 14:47:01
diff --git a/MD5 b/MD5
new file mode 100644
index 0000000..17e699c
--- /dev/null
+++ b/MD5
@@ -0,0 +1,12 @@
+d3fa775b284a9f022c9b770ecd9285bc *DESCRIPTION
+8b54e5a89fbda3af5e077053d40bec76 *NAMESPACE
+f7c653af4ae99ad2374fa6302e086a2b *data/datalist
+6eabd3cb5216163d31339f6ed92910a4 *data/ge03d2.RData
+d4923046420c507178d81c61c6c69884 *data/ge03d2.clean.RData
+8f3d6948e3858ec19a7975fadef18e84 *data/ge03d2c.RData
+a9542a2c6a4303143d3cb5d6256414c6 *data/ge03d2ex.RData
+201d22b870f4b67d1ee12a4504a70b63 *data/ge03d2ex.clean.RData
+a1a9087e6143c7c1c727387bc7d0e653 *data/srdta.RData
+e5305b4d8b0ec48acd8f944b13fdfc67 *man/GenABEL.data-package.Rd
+d92de354f54187c48c9213656eb0e037 *man/ge03d2.Rd
+ec02785b863f24d9cdb5aa75ea3f01de *man/srdta.Rd
diff --git a/NAMESPACE b/NAMESPACE
new file mode 100644
index 0000000..d75f824
--- /dev/null
+++ b/NAMESPACE
@@ -0,0 +1 @@
+exportPattern("^[[:alpha:]]+")
diff --git a/data/datalist b/data/datalist
new file mode 100644
index 0000000..2df8316
--- /dev/null
+++ b/data/datalist
@@ -0,0 +1,6 @@
+ge03d2: ge03d2 pop2.ids qc.nostr qc.str
+ge03d2.clean
+ge03d2c
+ge03d2ex
+ge03d2ex.clean
+srdta
diff --git a/data/ge03d2.RData b/data/ge03d2.RData
new file mode 100644
index 0000000..4ff11ff
Binary files /dev/null and b/data/ge03d2.RData differ
diff --git a/data/ge03d2.clean.RData b/data/ge03d2.clean.RData
new file mode 100644
index 0000000..093b75c
Binary files /dev/null and b/data/ge03d2.clean.RData differ
diff --git a/data/ge03d2c.RData b/data/ge03d2c.RData
new file mode 100644
index 0000000..08dd1aa
Binary files /dev/null and b/data/ge03d2c.RData differ
diff --git a/data/ge03d2ex.RData b/data/ge03d2ex.RData
new file mode 100644
index 0000000..0b4da60
Binary files /dev/null and b/data/ge03d2ex.RData differ
diff --git a/data/ge03d2ex.clean.RData b/data/ge03d2ex.clean.RData
new file mode 100644
index 0000000..d2a089c
Binary files /dev/null and b/data/ge03d2ex.clean.RData differ
diff --git a/data/srdta.RData b/data/srdta.RData
new file mode 100644
index 0000000..9160dcc
Binary files /dev/null and b/data/srdta.RData differ
diff --git a/debian/README.source b/debian/README.source
deleted file mode 100644
index 1bb8683..0000000
--- a/debian/README.source
+++ /dev/null
@@ -1,59 +0,0 @@
-Explanation for binary files inside source package according to
- http://lists.debian.org/debian-devel/2013/09/msg00332.html
-
-This package is a pure collection of data which is needed to
- 1. Build r-cran-genabel >= 1.8
- 2. Run unit tests in autopkgtest for r-cran-genabel
-
-Here comes a description of the single data files:
-
-Files: data/*
-Documentation: man/GenABEL.data-package.Rd
- GenABEL.data contains six files with data which is used by examples of GenABEL.
- These are ge03d2.clean.RData, ge03d2c.RData, ge03d2ex.clean.RData, ge03d2ex.RData, ge03d2.RData and srdta.RData.
-
-Files: data/ge03d2.Rdata
-Documentation: man/ge03d2.Rd
- A small data set (approximately 1,000 people and 8,000 SNPs) containing
- data on 3 autosomes and X chromsome. Is a good set for
- demonatration of the QC procedures (different genotyping errors
- are introduced) and GWA analysis.
- This data set was developed for the "Advances in population-
- based studies" (Ge03) course of the Nihes.
-
-Files: data/ge03d2c.Rdata
-Documentation: man/ge03d2.Rd
- A small data set (approximately 200 people and 8,000 SNPs) containing
- data on 3 autosomes and X chromsome. This data set is
- complementary to ge03d2.
-
-Files: data/ge03d2ex.Rdata
-Documentation: man/ge03d2.Rd
- A small data set (approximately 150 people and 4,000 SNPs) containing
- data on 3 autosomes and X chromsome. Is a good set for
- demonatration of the QC procedures (different genotyping errors
- are introduced) and GWA analysis.
- This data set was developed for the "Advances in population-
- based studies" (Ge03) course of the Nihes.
- See vignette "GenABEL-tutorial.pdf" in the r-cran-genabel package
- for details.
-
-Files: data/*.clean.Rdata
-Documentation: man/ge03d2.Rd
- The data sets with extension ".clean" are sets after QC.
-
-Files: data/srdta.RData
-Documentation: man/srdta.Rd
- srdta contains gwaa.data object with results
- on a small region of
- about 2.5 Mb. 833 SNPs are typed on 2500 people.
- NA rate is 95\%. Sex, age, two quantitative (qt1 and
- qt2) and one binary (bt) traits are available for
- analysis.
- Original data files used for this set are available as
- srphenos.dat (phenotypes), srgenos.dat (human-readable
- genotypes) and srgenos.raw (genotypes in internal format)
-
-
- -- Andreas Tille <tille at debian.org> Fri, 20 Jun 2014 09:23:44 +0200
-
diff --git a/debian/changelog b/debian/changelog
deleted file mode 100644
index 199103d..0000000
--- a/debian/changelog
+++ /dev/null
@@ -1,5 +0,0 @@
-r-cran-genabel.data (1.0.0-1) unstable; urgency=low
-
- * Initial release (Closes: #752153).
-
- -- Andreas Tille <tille at debian.org> Fri, 20 Jun 2014 09:23:44 +0200
diff --git a/debian/compat b/debian/compat
deleted file mode 100644
index ec63514..0000000
--- a/debian/compat
+++ /dev/null
@@ -1 +0,0 @@
-9
diff --git a/debian/control b/debian/control
deleted file mode 100644
index 7d4c3db..0000000
--- a/debian/control
+++ /dev/null
@@ -1,27 +0,0 @@
-Source: r-cran-genabel.data
-Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Andreas Tille <tille at debian.org>
-Section: gnu-r
-Priority: optional
-Build-Depends: debhelper (>= 9),
- cdbs,
- r-base-dev
-Standards-Version: 3.9.5
-Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/R/r-cran-genabel.data/trunk/
-Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/R/r-cran-genabel.data/trunk/
-Homepage: http://cran.at.r-project.org/web/packages/GenABEL.data/
-
-Package: r-cran-genabel.data
-Architecture: any
-Depends: ${shlibs:Depends},
- ${R:Depends}
-Description: data package for genome-wide SNP association analysis
- The package offers the R library GenABEL for the hunt of genetic contributions
- to a disease (or any other pheonypical trait) by so called genome-wide
- association analysis. Additional input commonly comes from DNA mircoarray
- experiments, performed on every individual, that determine differences
- (polymorphisms) in the population. GenABEL finds associations between
- quantitative or binary traits and single-nucleiotide polymorphisms
- (SNPs).
- .
- GenABEL.data package consists of a data set used by GenABEL functions.
diff --git a/debian/copyright b/debian/copyright
deleted file mode 100644
index 389a0b7..0000000
--- a/debian/copyright
+++ /dev/null
@@ -1,30 +0,0 @@
-Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
-Upstream-Name: GenABEL.data
-Upstream-Contact: Maksim Struchalin <m.v.struchalin at mail.ru>
-Source: http://cran.at.r-project.org/web/packages/GenABEL.data/
-
-Files: *
-Copyright: 2013 Maksim Struchalin <m.v.struchalin at mail.ru>
-License: GPL-2+
-
-Files: debian/*
-Copyright: 2014 Andreas Tille <tille at debian.org>
-License: GPL-2+
-
-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.
-
diff --git a/debian/rules b/debian/rules
deleted file mode 100755
index 2fbba2d..0000000
--- a/debian/rules
+++ /dev/null
@@ -1,3 +0,0 @@
-#!/usr/bin/make -f
-
-include /usr/share/R/debian/r-cran.mk
diff --git a/debian/source/format b/debian/source/format
deleted file mode 100644
index 163aaf8..0000000
--- a/debian/source/format
+++ /dev/null
@@ -1 +0,0 @@
-3.0 (quilt)
diff --git a/debian/watch b/debian/watch
deleted file mode 100644
index 4420e08..0000000
--- a/debian/watch
+++ /dev/null
@@ -1,2 +0,0 @@
-version=3
-http://cran.r-project.org/src/contrib/GenABEL.data_(.*)\.tar\.gz
diff --git a/man/GenABEL.data-package.Rd b/man/GenABEL.data-package.Rd
new file mode 100644
index 0000000..58f5274
--- /dev/null
+++ b/man/GenABEL.data-package.Rd
@@ -0,0 +1,36 @@
+\name{GenABEL.data-package}
+\alias{GenABEL.data-package}
+\alias{GenABEL.data}
+\docType{package}
+\title{
+GenABEL.data: An R package for storing GenABEL data
+}
+\description{
+GenABEL.data contains six files with data which is used by examples of GenABEL.
+These are ge03d2.clean.RData, ge03d2c.RData, ge03d2ex.clean.RData, ge03d2ex.RData, ge03d2.RData and srdta.RData.
+The files are the same as they were GenABEL package.
+
+}
+\details{
+\tabular{ll}{
+Package: \tab GenABEL.data\cr
+Type: \tab Package\cr
+Version: \tab 1.0\cr
+Date: \tab 2013-11-27\cr
+License: \tab GPL (>= 2)\cr
+}
+GenABEL.data package can be used only together with GenABEL package.
+}
+\author{
+Authors: Maksim Struchalin <m.v.struchalin at mail.ru> and GenABEL project developers <genabel.project at gmail.com>
+}
+\references{
+www.genabel.org
+}
+\keyword{ package }
+\seealso{
+GenABEL
+}
+\examples{
+data(srdta)
+}
diff --git a/man/ge03d2.Rd b/man/ge03d2.Rd
new file mode 100644
index 0000000..9f2a0e5
--- /dev/null
+++ b/man/ge03d2.Rd
@@ -0,0 +1,55 @@
+\name{ge03d2}
+\alias{ge03d2}
+\alias{ge03d2.clean}
+\alias{ge03d2c}
+\alias{ge03d2ex}
+\alias{ge03d2ex.clean}
+\alias{pop2.ids}
+\alias{qc.nostr}
+\alias{qc.str}
+\docType{data}
+\title{GWA-type data on few small region}
+\description{
+ \code{ge03d2}
+ A small data set (approximately 1,000 people and 8,000 SNPs) containing
+ data on 3 autosomes and X chromsome. Is a good set for
+ demonatration of the QC procedures (different genotyping errors
+ are introduced) and GWA analysis. Run demo(ge03d2) to see a demo.
+ This data set was developed for the "Advances in population-
+ based studies" (Ge03) course of the Nihes.
+
+ \code{ge03d2c}
+ A small data set (approximately 200 people and 8,000 SNPs) containing
+ data on 3 autosomes and X chromsome. This data set is
+ complementary to \code{\link{ge03d2}}.
+
+ \code{ge03d2ex}
+ A small data set (approximately 150 people and 4,000 SNPs) containing
+ data on 3 autosomes and X chromsome. Is a good set for
+ demonatration of the QC procedures (different genotyping errors
+ are introduced) and GWA analysis.
+ This data set was developed for the "Advances in population-
+ based studies" (Ge03) course of the Nihes.
+ See vignette "GenABEL-tutorial.pdf" for details.
+
+ The data sets with extension ".clean" are sets after QC.
+}
+\usage{data(ge03d2)}
+%\format{
+%}
+%\details{
+%}
+%\source{
+%}
+%\references{
+%}
+\examples{
+#main example: use this to see full functionality
+# demo(ge03d2)
+
+# load and work with ge03d2
+data(ge03d2)
+#a <- qtscore(dm2,ge03d2)
+#plot(a)
+}
+\keyword{datasets}
diff --git a/man/srdta.Rd b/man/srdta.Rd
new file mode 100644
index 0000000..193a263
--- /dev/null
+++ b/man/srdta.Rd
@@ -0,0 +1,42 @@
+\name{srdta}
+\alias{srdta}
+\docType{data}
+\title{GWA-type data on small region}
+\description{
+ \code{srdta} contains gwaa.data object with results
+ on a small region of
+ about 2.5 Mb. 833 SNPs are typed on 2500 people.
+ NA rate is 95\%. Sex, age, two quantitative (qt1 and
+ qt2) and one binary (bt) traits are available for
+ analysis. Run demo(srdta) and check tut-srdta.pdf
+ to see examples of work with this data set.
+ Original data files used for this set are located at
+ YOUR\_R\_LIB\_LOCATION/exdata/srphenos.dat (phenotypes),
+ srgenos.dat (human-readable genotypes) and srgenos.raw
+ (genotypes in internal format)}
+\usage{data(srdta)}
+\format{
+ Standard object of class \code{gwaa.data-class} (see the GenABEL manual).
+}
+%\details{
+%}
+%\source{
+%}
+%\references{
+%}
+\examples{
+
+#\dontrun{
+#demo(srdta)
+#}
+
+# load and work with srdta
+data(srdta)
+# truncate the data to make the example faster
+#srdta <- srdta[seq(from=1,to=nids(srdta),by=2),seq(from=1,to=nsnps(srdta),by=2)]
+#mc <- check.marker(data=gtdata(srdta)[,1:100],redundant="all",
+# maf=0.01,minconcordance=0.9,fdr=.1,ibs.mrk=0)
+#plot(mc)
+#check.trait(names(phdata(srdta)),srdta)
+}
+\keyword{datasets}
--
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