[adegenet-commits] r903 - pkg/R

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

Author: jombart
Date: 2011-06-13 12:50:39 +0200 (Mon, 13 Jun 2011)
New Revision: 903

Modified:
   pkg/R/import.R
Log:
All snps are well extracted. Need to keep missing data now.


Modified: pkg/R/import.R
===================================================================
--- pkg/R/import.R	2011-06-10 17:47:12 UTC (rev 902)
+++ pkg/R/import.R	2011-06-13 10:50:39 UTC (rev 903)
@@ -1100,7 +1100,9 @@
 
 
     ## analyse pool of alleles
-    POOL <- lapply(POOL, setdiff, "-")
+    letterOK <- c("a","g","c","t","A","G","C","T")
+    POOL <- lapply(POOL, function(e) e[e %in% letterOK]) # keep only proper letters
+    ## POOL <- lapply(POOL, setdiff, "-")
     nb.alleles <- sapply(POOL, length)
     snp.posi <- nb.alleles==2
     sec.all <- unlist(lapply(POOL[snp.posi], function(e) e[2]))