[Gtdb-commits] r19 - pkg/gt.db/man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sun Oct 18 02:04:53 CEST 2009
Author: dahinds
Date: 2009-10-18 02:04:52 +0200 (Sun, 18 Oct 2009)
New Revision: 19
Added:
pkg/gt.db/man/gt.demo.check.Rd
pkg/gt.db/man/init.gt.db.Rd
Modified:
pkg/gt.db/man/demo_01.Rd
pkg/gt.db/man/demo_02.Rd
pkg/gt.db/man/hapmap.Rd
pkg/gt.db/man/use.gt.db.Rd
Log:
- added new help pages for gt.demo.check and init.gt.db
- updated hapmap.Rd, added examples to demo_*.Rd
- added link to use.gt.db page
Modified: pkg/gt.db/man/demo_01.Rd
===================================================================
--- pkg/gt.db/man/demo_01.Rd 2009-10-17 23:57:20 UTC (rev 18)
+++ pkg/gt.db/man/demo_01.Rd 2009-10-18 00:04:52 UTC (rev 19)
@@ -42,4 +42,8 @@
The International HapMap Project. \url{http://www.hapmap.org}.
}
+\examples{\dontrun{
+# load demo datasets into GT.DB
+demo('setup.gt.demo')
+}}
\keyword{datasets}
Modified: pkg/gt.db/man/demo_02.Rd
===================================================================
--- pkg/gt.db/man/demo_02.Rd 2009-10-17 23:57:20 UTC (rev 18)
+++ pkg/gt.db/man/demo_02.Rd 2009-10-18 00:04:52 UTC (rev 19)
@@ -38,4 +38,8 @@
The International HapMap Project. \url{http://www.hapmap.org}.
}
+\examples{\dontrun{
+# load demo datasets into GT.DB
+demo('setup.gt.demo')
+}}
\keyword{datasets}
Added: pkg/gt.db/man/gt.demo.check.Rd
===================================================================
--- pkg/gt.db/man/gt.demo.check.Rd (rev 0)
+++ pkg/gt.db/man/gt.demo.check.Rd 2009-10-18 00:04:52 UTC (rev 19)
@@ -0,0 +1,41 @@
+%
+% Copyright (C) 2009, Perlegen Sciences, Inc.
+%
+% Written by David A. Hinds <dhinds at sonic.net>
+%
+% This 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 3 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, see <http://www.gnu.org/licenses/>
+%
+\name{gt.demo.check}
+\alias{gt.demo.check}
+\title{Check for Presence of GT.DB Demo Datasets}
+\description{
+ This is used in many of the GT.DB examples to check for the presence
+ of the demo datasets.
+}
+\usage{
+gt.demo.check()
+}
+\details{
+ If the demo datasets are unavailable, then the example code is
+ terminated with an error message. If invoked non-interactively (say,
+ from \code{R CMD CHECK}), then a temporary SQLite database is created
+ for the demo datasets.
+}
+\seealso{
+ \code{\link{init.gt.db}}, \code{\link{demo}(setup.gt.demo)}.
+}
+\examples{
+gt.demo.check()
+}
+\keyword{database}
Modified: pkg/gt.db/man/hapmap.Rd
===================================================================
--- pkg/gt.db/man/hapmap.Rd 2009-10-17 23:57:20 UTC (rev 18)
+++ pkg/gt.db/man/hapmap.Rd 2009-10-18 00:04:52 UTC (rev 19)
@@ -19,15 +19,22 @@
\name{hapmap}
\docType{data}
\alias{hapmap.subjects}
-\title{Data from the International HapMap Project}
+\title{Subject Data from the International HapMap Project}
\description{
- \code{hapmap.subjects} describes the sample plate and panel
- membership, and parent/child relationships, for the 270 individuals
- genotyped in the Phase I and Phase II HapMap Projects.
+ \code{hapmap.subjects} describes sample plate and panel membership,
+ and parent/child relationships, for the 1301 individuals genotyped in
+ the Phase II and Phase III HapMap Projects.
}
\usage{data(hapmap)}
\source{The International HapMap Project}
\references{
The International HapMap Project. \url{http://www.hapmap.org}.
}
+\seealso{
+ \code{\link{demo}(setup.hapmap)}.
+}
+\examples{\dontrun{
+# create HapMap project in GT.DB
+demo('setup.hapmap')
+}}
\keyword{datasets}
Added: pkg/gt.db/man/init.gt.db.Rd
===================================================================
--- pkg/gt.db/man/init.gt.db.Rd (rev 0)
+++ pkg/gt.db/man/init.gt.db.Rd 2009-10-18 00:04:52 UTC (rev 19)
@@ -0,0 +1,50 @@
+%
+% Copyright (C) 2009, Perlegen Sciences, Inc.
+%
+% Written by David A. Hinds <dhinds at sonic.net>
+%
+% This 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 3 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, see <http://www.gnu.org/licenses/>
+%
+\name{init.gt.db}
+\alias{init.gt.db}
+\title{Initialize GT.DB Database}
+\description{
+ Create all the standard GT.DB database objects (tables, indexes) in an
+ empty database.
+}
+\usage{
+init.gt.db()
+}
+\details{
+ This should be called after connecting to a new database using
+ \code{\link[DBI:dbConnect]{dbConnect}} and \code{\link{use.gt.db}}.
+ Scripts for creating GT.DB tables and indexes are installed under
+ \code{library(help='gt.db')$path} in the \file{schema} subdirectory.
+}
+\seealso{
+ \code{\link[DBI:dbConnect]{dbConnect}},
+ \code{\link{use.gt.db}},
+ \code{\link{demo}(setup.gt.demo)}.
+}
+\examples{\dontrun{
+# create new SQLite database in a temporary file
+fn <- tempfile()
+dbx <- dbConnect(dbDriver('SQLite'), fn)
+# unlink it so it will go away at the end of the session
+unlink(fn)
+use.gt.db(dbx)
+init.gt.db()
+demo('setup.gt.demo')
+}}
+\keyword{database}
Modified: pkg/gt.db/man/use.gt.db.Rd
===================================================================
--- pkg/gt.db/man/use.gt.db.Rd 2009-10-17 23:57:20 UTC (rev 18)
+++ pkg/gt.db/man/use.gt.db.Rd 2009-10-18 00:04:52 UTC (rev 19)
@@ -36,7 +36,8 @@
}
\seealso{
\code{\link[DBI:dbDriver]{dbDriver}},
- \code{\link[DBI:dbConnect]{dbConnect}}.
+ \code{\link[DBI:dbConnect]{dbConnect}},
+ \code{\link{init.gt.db}}.
}
\examples{\dontrun{
library(RSQLite)
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