Typos fixed

fischuu · Sep 6, 2016 · e30bdbe · e30bdbe
1 parent 68d4f4a
commit e30bdbe
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Showing 8 changed files with 10 additions and 38 deletions.
diff --git a/R/importVCF.R b/R/importVCF.R
@@ -1,4 +1,8 @@
 importVCF <- function(file, na.seq="./."){
+# Necessary variable declaration for Cran checks
+  V3 <- NULL
+  rn <- NULL
+
  # First read in the header lines and determine the skip variable for the body
   con <- file(file) 
   open(con);
@@ -87,5 +91,5 @@ importVCF <- function(file, na.seq="./."){
 #tmp2 <- importVCF(file="/home/ejo138/ownCloud/Luke/Projects/Consulting/Dog-Liver/Data/NWT_151110.vcf")
 #tmp2
 
-genotDataVCF <- importVCF(file="/home/ejo138/ownCloud/R-Packages-Pages/GenomicTools/Datasets/genotypes.vcf")
-save(genotDataVCF, file="/home/ejo138/GitHub/GenomicTools/data/genotDataVCF.rda")
+#genotDataVCF <- importVCF(file="/home/ejo138/ownCloud/R-Packages-Pages/GenomicTools/Datasets/genotypes.vcf")
+#save(genotDataVCF, file="/home/ejo138/GitHub/GenomicTools/data/genotDataVCF.rda")
diff --git a/R/print.vcf.R b/R/print.vcf.R
@@ -14,7 +14,7 @@
 # Print the header
   cat("First",n,"rows of $header:\n\n")  
   if(fullHeader){
-    for(i in 1:length(header)){
+    for(i in 1:nHeader){
       cat(x$header[i],"\n")
     }
   } else {

diff --git a/data/genotDataVCF.rda b/data/genotDataVCF.rda
diff --git a/man/genotDataVCF.Rd b/man/genotDataVCF.Rd
diff --git a/src/GenomicTools.so b/src/GenomicTools.so
diff --git a/src/mdr.o b/src/mdr.o
diff --git a/src/timeCluster.o b/src/timeCluster.o
diff --git a/vignettes/GenomicTools-Vignette.Rmd b/vignettes/GenomicTools-Vignette.Rmd
@@ -112,17 +112,11 @@ and the first rows of it look like this
 genotData
 ```
 
-The same file is also as vcf available. Here, the preloaded file can be made available with
+On 
 
-```{r}
-data("genotDataVCF")
-```
-
-and the first rows of it look like this
+http://genomictools.danielfischer.name
 
-```{r, comment=NA}
-genotDataVCF
-```
+are also example vcf files available, that were too large to include into the package.
 
 ### An own ped/map filepair
 An own filepair of ped/map files can be loaded, using the `importPED()` command: