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VascoElbrecht · Mar 27, 2018 · 444e7b8 · 444e7b8
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diff --git a/PrimerMiner/DESCRIPTION b/PrimerMiner/DESCRIPTION
@@ -2,7 +2,7 @@ Package: PrimerMiner
 Type: Package
 Title: PrimerMiner an R package for development and in silico validation of DNA metabarcoding primers
 Version: 0.17
-Date: 2018-02-13
+Date: 2018-03-27
 Author: Vasco Elbrecht
 Maintainer: Vasco Elbrecht <[email protected]>
 Description: PrimerMiner is a R based batch sequence downloader to design and verify metabarcoding primers. Sequences for a specified marker (e.g. COI) are obtained from NCBI and BOLD and clustered into Operational taxonomic units (OTU) to reduce bias introduced by over represented sequences in the data bases.

diff --git a/PrimerMiner/man/primerversions.Rd b/PrimerMiner/man/primerversions.Rd
@@ -3,7 +3,7 @@
 \title{
 Converting degenerated primers into their unique versions}
 \description{
-Degenerated primers contain varriable possions, wich makes them better matching towards different template DNAs that are commonly presend in metabarcoding bulk samples. Here we take the IUPAC Codes that define the degenerated bases (e.g. \code{Y} stands for 	\code{C} or \code{T}) and convert them back to the standard bases \code{C}, \code{G}, \code{A} & \code{T}. The function takes in one string of characters (the primer sequence), and retunes all possible primer versions.
+Degenerated primers contain variable posstions, wich makes them better matching towards different template DNAs that are commonly present in metabarcoding bulk samples. Here we take the IUPAC Codes that define the degenerated bases (e.g. \code{Y} stands for 	\code{C} or \code{T}) and convert them back to the standard bases \code{C}, \code{G}, \code{A} & \code{T}. The function takes in one string of characters (the primer sequence), and retunes all possible primer versions.
 
 The primer sequence can also be returned as reverse complement with \code{fw=F} and iosine \code{I} bases are treated as \code{N} by default (can be turned off with \code{convertInosine=T}).
 
@@ -12,24 +12,8 @@ The primer sequence can also be returned as reverse complement with \code{fw=F}
 primerversions(primer, fw=T, convertInosine=T)
 }
 \arguments{
-  \item{primer}{Primer sequence in qoutemarkes and upper case letters.}
+  \item{primer}{Primer sequence in quotemarks and upper case letters.}
   \item{fw}{Primer is oriented in forward direction 5->3, should usually be the case. But also the reverse complement can be retuned by setting \code{fw=F}}
   \item{id}{
 Inosine \code{I} are usually treated as \code{N} and converted into \code{C}, \code{G}, \code{A} & \code{T}. To keep the iosine, set \code{convertInosine=F}}
-}
-\details{
-
-\value{
-}
-\references{
-}
-\author{
-}
-\note{
-}
-
-
-\seealso{
-\code{\link{}}
-}
-\examples{}
+} 
diff --git a/Sample_Data/package_tutorial.R b/Sample_Data/package_tutorial.R
@@ -65,5 +65,6 @@ primer_threshold("save_evaluation_table_LCO.csv", "save_evaluation_table_BR1.csv
 
 
 
-
+# generate different primer versions that are contained in a degenerated primer
+primerversions("GCHCCHGAYATRGCHTTYCC") # BF2
Original file line number	Diff line number	Diff line change
Expand Up		@@ -65,5 +65,6 @@ primer_threshold("save_evaluation_table_LCO.csv", "save_evaluation_table_BR1.csv




		# generate different primer versions that are contained in a degenerated primer
		primerversions("GCHCCHGAYATRGCHTTYCC") # BF2