[Gtdb-commits] r39 - in pkg/gt.db: . R inst/doc man

[noreply at r-forge.r-project.org]

Author: dahinds
Date: 2010-02-22 06:37:02 +0100 (Mon, 22 Feb 2010)
New Revision: 39

Modified:
   pkg/gt.db/DESCRIPTION
   pkg/gt.db/R/assay.R
   pkg/gt.db/R/genotype.R
   pkg/gt.db/inst/doc/gt.db.pdf
   pkg/gt.db/man/load.affy.chp.data.Rd
   pkg/gt.db/man/load.hapmap.data.Rd
Log:
- Minor code and help cleanups
- Bumped version number
- Updated PDF manual



Modified: pkg/gt.db/DESCRIPTION
===================================================================
--- pkg/gt.db/DESCRIPTION	2010-02-21 23:10:40 UTC (rev 38)
+++ pkg/gt.db/DESCRIPTION	2010-02-22 05:37:02 UTC (rev 39)
@@ -1,6 +1,6 @@
 Package: gt.db
-Version: 0.5-1
-Date: 2009-10-08
+Version: 0.6-1
+Date: 2010-02-21
 Title: GT.DB: Genotype Data Management and Analysis
 Author: David Hinds
 Maintainer: David Hinds <dhinds at sonic.net>
@@ -8,5 +8,4 @@
   phenotype data, and association study results
 License: GPL
 Depends: R (>= 2.7.0), lattice, grid, methods, DBI
-Suggests: nlme, cluster, mda, ROracle, RMySQL, RSQLite
-Packaged: Thu Oct  8 15:22:32 2009; dhinds
+Suggests: nlme, cluster, mda, RMySQL, RSQLite

Modified: pkg/gt.db/R/assay.R
===================================================================
--- pkg/gt.db/R/assay.R	2010-02-21 23:10:40 UTC (rev 38)
+++ pkg/gt.db/R/assay.R	2010-02-22 05:37:02 UTC (rev 39)
@@ -163,9 +163,9 @@
     tx.mode <- .gt.db.options('tx.mode')
     if ((db.mode == tx.mode) ||
         all(is.na(data$qscore) && is.na(data$raw.data))) {
-        cvt.fn <- ''
+        raw.fn <- ''
     } else if (db.mode == 'raw' && tx.mode == 'hex') {
-        cvt.fn <- ':unhex:'
+        raw.fn <- ':unhex:'
     } else {
         stop('unknown conversion!')
     }
@@ -173,7 +173,7 @@
     sql <-
      'insert into assay_data
       values (null,:1,:2,:3,:4,%1$s(:5),%1$s(:6))'
-    sql <- sprintf(sql, cvt.fn)
+    sql <- sprintf(sql, raw.fn)
     cols <- c('assay.id','flags','genotype','qscore','raw.data')
     sql.exec(gt.db::.gt.db, sql, dset.id, data[cols], progress=progress)
 }

Modified: pkg/gt.db/R/genotype.R
===================================================================
--- pkg/gt.db/R/genotype.R	2010-02-21 23:10:40 UTC (rev 38)
+++ pkg/gt.db/R/genotype.R	2010-02-22 05:37:02 UTC (rev 39)
@@ -52,9 +52,9 @@
     if (genotype)
         sql <- paste(sql, ', :clob:(genotype)')
     if (qscore)
-        sql <- paste(sql, ', ', cvt.fn, '(qscore)', sep='')
+        sql <- sprintf("%s, %s(qscore)", sql, cvt.fn)
     if (raw.data)
-        sql <- paste(sql, ', ', cvt.fn, '(raw_data)', sep='')
+        sql <- sprintf("%s, %s(raw_data)", sql, cvt.fn)
 
     sql <- paste(sql,
      'from assay_data d, assay a, assay_position p

Modified: pkg/gt.db/inst/doc/gt.db.pdf
===================================================================
(Binary files differ)


Property changes on: pkg/gt.db/inst/doc/gt.db.pdf
___________________________________________________________________
Name: svn:mime-type
   + application/pdf

Modified: pkg/gt.db/man/load.affy.chp.data.Rd
===================================================================
--- pkg/gt.db/man/load.affy.chp.data.Rd	2010-02-21 23:10:40 UTC (rev 38)
+++ pkg/gt.db/man/load.affy.chp.data.Rd	2010-02-22 05:37:02 UTC (rev 39)
@@ -29,14 +29,16 @@
 \arguments{
   \item{dataset}{the unique identifier of the dataset to receive the
     genotype data.}
-  \item{anno}{an annotation data frame from \code{\link{load.affy.chp.data}}.}
-  \item{files}{a vector of all the text CHP files to be imported.}
+  \item{anno}{an annotation data frame from \code{\link{read.affy.anno}}.}
+  \item{files}{a character vector of all the text CHP file names to be
+    imported.}
   \item{progress}{logical: indicates whether to report progress during
     the database load.}
 }
 \details{
   The input files should be tab-delimited text versions of CHP files as
-  created by \code{apt-chp-to-txt} in the Affymetrix Power Tools.
+  created by the \code{apt-chp-to-txt} utility from the Affymetrix Power
+  Tools.
 
   Loading CHP data is a two stage process.  In the first stage, we
   reorganize the input data into new files that represent all samples
@@ -44,10 +46,9 @@
   these files into the database.  The two stages effectively allow us to
   perform an \dQuote{out-of-core} transpose of the genotype matrix,
   because we typically will not be able to hold an entire genotype
-  dataset for a large study in working memory.  The temporary files
-  require about 20\% of the space of the original text CHP files.  They
-  are created in the current directory and deleted at the end of the
-  import.
+  dataset for a large study in memory.  The temporary files require
+  about 20\% of the space of the original text CHP files.  They are
+  created in the current directory and deleted at the end of the import.
 
   When creating a dataset to receive CHP data, be sure to specify
   \code{raw.format='chpdata'}.

Modified: pkg/gt.db/man/load.hapmap.data.Rd
===================================================================
--- pkg/gt.db/man/load.hapmap.data.Rd	2010-02-21 23:10:40 UTC (rev 38)
+++ pkg/gt.db/man/load.hapmap.data.Rd	2010-02-22 05:37:02 UTC (rev 39)
@@ -32,10 +32,11 @@
   \item{verbose}{logical: indicates whether to report progress.}
 }
 \details{
-  This function supports loading recent Phase 2 and Phase 3 genotype
-  files.  If files include data from several population panels, then the
-  genotype data is merged into a single dataset spanning all those
-  panels.  Only non-redundant forward-orientation files are supported.
+  This function supports loading recent HapMap Phase II and Phase III
+  genotype files.  If files include data from several population panels,
+  then the genotype data is merged into a single dataset spanning all
+  those panels.  Only non-redundant forward-orientation files are
+  supported.
 }
 \seealso{
   \code{\link{hapmap.subjects}}.