[Genabel-commits] r1420 - in pkg: . GenABEL.data GenABEL.data/data GenABEL.data/inst GenABEL.data/inst/extdata GenABEL.data/man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Nov 27 17:53:32 CET 2013
Author: maksim
Date: 2013-11-27 17:53:31 +0100 (Wed, 27 Nov 2013)
New Revision: 1420
Added:
pkg/GenABEL.data/
pkg/GenABEL.data/DESCRIPTION
pkg/GenABEL.data/NAMESPACE
pkg/GenABEL.data/data/
pkg/GenABEL.data/data/datalist
pkg/GenABEL.data/data/ge03d2.RData
pkg/GenABEL.data/data/ge03d2.clean.RData
pkg/GenABEL.data/data/ge03d2c.R
pkg/GenABEL.data/data/ge03d2ex.R
pkg/GenABEL.data/data/ge03d2ex.clean.RData
pkg/GenABEL.data/data/srdta.R
pkg/GenABEL.data/inst/
pkg/GenABEL.data/inst/extdata/
pkg/GenABEL.data/inst/extdata/ge03d2c_id_names.txt
pkg/GenABEL.data/inst/extdata/ge03d2c_snp_names.txt
pkg/GenABEL.data/inst/extdata/ge03d2ex_id_names.txt
pkg/GenABEL.data/inst/extdata/ge03d2ex_snp_names.txt
pkg/GenABEL.data/inst/extdata/srgenos.dat
pkg/GenABEL.data/inst/extdata/srphenos.dat
pkg/GenABEL.data/man/
pkg/GenABEL.data/man/GenABEL.data-package.Rd
pkg/GenABEL.data/man/ge03d2.Rd
pkg/GenABEL.data/man/srdta.Rd
Log:
The package GenABEL.data contains the data from GenABEL/data/ and some data from GenABEL/inst/exdata/ directories which are used by GenABEL examples and Runit tests. Removing this data from GenABEL package was requested by CRAN people because the package size was to big. In this version of GenABEL.data, the files srdta.RData, ge03d2ex.R and ge03d2c.R are generated during R CMD build process. The files ge03d2.clean.RData, ge03d2ex.clean.RData and ge03d2.RData are copied from GenABEL/data.
Added: pkg/GenABEL.data/DESCRIPTION
===================================================================
--- pkg/GenABEL.data/DESCRIPTION (rev 0)
+++ pkg/GenABEL.data/DESCRIPTION 2013-11-27 16:53:31 UTC (rev 1420)
@@ -0,0 +1,13 @@
+Package: GenABEL.data
+Type: Package
+Title: Package contains data which is used by GenABEL example and test functions
+Version: 1.0
+Date: 2013-11-27
+Authors at R: c(person("Maksim Struchalin", "Developer", role = c("aut", "cre"), email = "m.v.struchalin at mail.ru"),
+ person("GenABEL project developers", "Developer", role = "aut", email = "genabel.project at gmail.com"))
+Depends: R (>= 2.15.0)
+Description: GenABEL.data package consists of a number of data files 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
+
Added: pkg/GenABEL.data/NAMESPACE
===================================================================
--- pkg/GenABEL.data/NAMESPACE (rev 0)
+++ pkg/GenABEL.data/NAMESPACE 2013-11-27 16:53:31 UTC (rev 1420)
@@ -0,0 +1 @@
+exportPattern("^[[:alpha:]]+")
Added: pkg/GenABEL.data/data/datalist
===================================================================
--- pkg/GenABEL.data/data/datalist (rev 0)
+++ pkg/GenABEL.data/data/datalist 2013-11-27 16:53:31 UTC (rev 1420)
@@ -0,0 +1,6 @@
+ge03d2: ge03d2 pop2.ids qc.nostr qc.str
+ge03d2.clean
+ge03d2c
+ge03d2ex
+ge03d2ex.clean
+srdta
Added: pkg/GenABEL.data/data/ge03d2.RData
===================================================================
(Binary files differ)
Property changes on: pkg/GenABEL.data/data/ge03d2.RData
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: pkg/GenABEL.data/data/ge03d2.clean.RData
===================================================================
(Binary files differ)
Property changes on: pkg/GenABEL.data/data/ge03d2.clean.RData
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: pkg/GenABEL.data/data/ge03d2c.R
===================================================================
--- pkg/GenABEL.data/data/ge03d2c.R (rev 0)
+++ pkg/GenABEL.data/data/ge03d2c.R 2013-11-27 16:53:31 UTC (rev 1420)
@@ -0,0 +1,48 @@
+#=====================================================================================
+#
+# Filename: ge03d2c.R
+#
+# Description: Generate ge03d2c.RData from the ge03d2.RData
+#
+# Version: 1.0
+# Created: 27-Nov-2013
+# Revision: none
+#
+#
+# Author: Maksim V. Struchalin
+# Company: YuriiA
+# Email: m.struch at mail.ru
+#
+#=====================================================================================
+
+
+
+if(require(GenABEL)) {
+
+# How we get id and snop names:
+#_____________________________
+#load("../../GenABEL/data/ge03d2c.RData")
+#snpnames_ge03d2c <- colnames(ge03d2c at gtdata)
+#idnames_ge03d2c <- rownames(ge03d2c at gtdata)
+#write.table(data.frame(snpnames_ge03d2c=snpnames_ge03d2c), file="../inst/extdata/ge03d2c_snp_names.txt", quote=F, row.names=F, col.names=T)
+#write.table(data.frame(idnames_ge03d2c=idnames_ge03d2c), file="../inst/extdata/ge03d2c_id_names.txt", quote=F, row.names=F, col.names=T)
+#_____________________________
+
+load("ge03d2.RData")
+adpr <- paste(getwd(), "/../inst/extdata/", sep="")
+snpnames_file <- paste(adpr, "ge03d2c_snp_names.txt", sep="")
+idnames_file <- paste(adpr, "ge03d2c_id_names.txt", sep="")
+
+snpnames_ge03d2c <- read.table(snpnames_file, header=T, strings=F)$snpnames_ge03d2c
+idnames_ge03d2c <- read.table(idnames_file, header=T, strings=F)$idnames_ge03d2c
+
+ge03d2c <- ge03d2[idnames_ge03d2c,snpnames_ge03d2c]
+
+rm(adpr, snpnames_ge03d2c, idnames_ge03d2c, ge03d2, pop2.ids, qc.nostr, qc.str)
+unlink(snpnames_file)
+unlink(idnames_file)
+
+
+} else {
+ error("GenABEL package should be installed. Try install.package(GenABEL).")
+}
Added: pkg/GenABEL.data/data/ge03d2ex.R
===================================================================
--- pkg/GenABEL.data/data/ge03d2ex.R (rev 0)
+++ pkg/GenABEL.data/data/ge03d2ex.R 2013-11-27 16:53:31 UTC (rev 1420)
@@ -0,0 +1,49 @@
+#=====================================================================================
+#
+# Filename: ge03d2ex.R
+#
+# Description: Generate ge03d2ex.RData from the ge03d2.RData
+#
+# Version: 1.0
+# Created: 27-Nov-2013
+# Revision: none
+#
+#
+# Author: Maksim V. Struchalin
+# Company: YuriiA
+# Email: m.struch at mail.ru
+#
+#=====================================================================================
+
+
+
+if(require(GenABEL)) {
+
+# How we get id and snop names:
+#_____________________________
+#load("ge03d2ex.RData")
+#snpnames_ge03d2ex <- colnames(ge03d2ex at gtdata)
+#idnames_ge03d2ex <- rownames(ge03d2ex at gtdata)
+#write.table(data.frame(snpnames_ge03d2ex=snpnames_ge03d2ex), file="ge03d2ex_snp_names.txt", quote=F, row.names=F, col.names=T)
+#write.table(data.frame(idnames_ge03d2ex=idnames_ge03d2ex), file="ge03d2ex_id_names.txt", quote=F, row.names=F, col.names=T)
+#_____________________________
+
+load("ge03d2.RData")
+adpr <- paste(getwd(), "/../inst/extdata/", sep="")
+
+snpnames_file <- paste(adpr, "ge03d2ex_snp_names.txt", sep="")
+idnames_file <- paste(adpr, "ge03d2ex_id_names.txt", sep="")
+
+snpnames_ge03d2ex <- read.table(snpnames_file, header=T, strings=F)$snpnames_ge03d2ex
+idnames_ge03d2ex <- read.table(idnames_file, header=T, strings=F)$idnames_ge03d2ex
+
+ge03d2ex <- ge03d2[idnames_ge03d2ex,snpnames_ge03d2ex]
+
+rm(adpr, snpnames_ge03d2ex, idnames_ge03d2ex, ge03d2, pop2.ids, qc.nostr, qc.str)
+unlink(snpnames_file)
+unlink(idnames_file)
+
+
+} else {
+ error("GenABEL package should be installed. Try install.package(GenABEL).")
+}
Added: pkg/GenABEL.data/data/ge03d2ex.clean.RData
===================================================================
(Binary files differ)
Property changes on: pkg/GenABEL.data/data/ge03d2ex.clean.RData
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: pkg/GenABEL.data/data/srdta.R
===================================================================
--- pkg/GenABEL.data/data/srdta.R (rev 0)
+++ pkg/GenABEL.data/data/srdta.R 2013-11-27 16:53:31 UTC (rev 1420)
@@ -0,0 +1,35 @@
+#=====================================================================================
+#
+# Filename: srdta.R
+#
+# Description: Generate srdta.RData from GenABEL/inst/extdata/srgenos.dat
+#
+# Version: 1.0
+# Created: 20-Nov-2013
+# Revision: none
+#
+#
+# Author: Maksim V. Struchalin
+# Company: YuriiA
+# Email: m.struch at mail.ru
+#
+#=====================================================================================
+
+
+
+if(require(GenABEL)) {
+adpr <- paste(getwd(), "/../inst/extdata/", sep="")
+genofile <- paste(adpr,"srgenos.dat",sep="")
+convert.snp.text(infile=genofile,outfile="srgenos.raw",bcast=200)
+phenofile <- paste(adpr,"srphenos.dat",sep="")
+srdta <- load.gwaa.data(geno="srgenos.raw",pheno=phenofile)
+unlink("srgenos.raw")
+
+unlink(genofile)
+unlink(phenofile)
+rm(adpr, genofile, phenofile)
+
+} else {
+ error("GenABEL package should be installed. Try install.package(GenABEL).")
+}
+
Added: pkg/GenABEL.data/inst/extdata/ge03d2c_id_names.txt
===================================================================
--- pkg/GenABEL.data/inst/extdata/ge03d2c_id_names.txt (rev 0)
+++ pkg/GenABEL.data/inst/extdata/ge03d2c_id_names.txt 2013-11-27 16:53:31 UTC (rev 1420)
@@ -0,0 +1,196 @@
+idnames_ge03d2c
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Added: pkg/GenABEL.data/inst/extdata/ge03d2c_snp_names.txt
===================================================================
--- pkg/GenABEL.data/inst/extdata/ge03d2c_snp_names.txt (rev 0)
+++ pkg/GenABEL.data/inst/extdata/ge03d2c_snp_names.txt 2013-11-27 16:53:31 UTC (rev 1420)
@@ -0,0 +1,7590 @@
+snpnames_ge03d2c
+rs1646456
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[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/genabel -r 1420
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