[Gtdb-commits] r21 - in pkg/gt.db: R man

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

Author: dahinds
Date: 2009-10-29 21:37:45 +0100 (Thu, 29 Oct 2009)
New Revision: 21

Modified:
   pkg/gt.db/R/sample.R
   pkg/gt.db/man/mk.sample.Rd
Log:
Added test, documented that sample positions are 1-based integers.


Modified: pkg/gt.db/R/sample.R
===================================================================
--- pkg/gt.db/R/sample.R	2009-10-18 01:23:29 UTC (rev 20)
+++ pkg/gt.db/R/sample.R	2009-10-29 20:37:45 UTC (rev 21)
@@ -58,6 +58,10 @@
         warning("sample positions are missing")
         data$position <- NA
     }
+    if (any(data$position < 1) ||
+        any(data$position != round(data$position))) {
+        stop("sample positions should be 1-based integers")
+    }
     sql.exec(gt.db::.gt.db, sql, dset.id, subj.id,
              data[c('sample.name','gender','position')])
 }

Modified: pkg/gt.db/man/mk.sample.Rd
===================================================================
--- pkg/gt.db/man/mk.sample.Rd	2009-10-18 01:23:29 UTC (rev 20)
+++ pkg/gt.db/man/mk.sample.Rd	2009-10-29 20:37:45 UTC (rev 21)
@@ -39,7 +39,8 @@
   \code{position}.  This information is important because it affects how
   various functions interpret genotyping data in this dataset.
   Sample gender is used to determine ploidy for sex linked assays, and
-  the position is used to parse arrays of packed genotype data.
+  the position is used to index arrays of packed genotype data.
+  Positions are 1-based integers.
 }
 \value{
 If successful, the number of rows inserted or deleted from the sample