#### *drop passing of ... arg to method snps<- eventually dispatches on

*doc'ed ... arg to GmapSnps constructor

*added aliases for snps<- when first arg is a GmapGenomeDirectory

*test case for creating a GmapGenome via a DNAStringSet was
broken. Example sequence was too short for gmap_build to work

Cory Barr authored on 12/09/2012 22:29:42
Showing 1 changed files
 ... ... @@ -25,8 +25,10 @@ Objects can be created by calls of the form \code{GmapSnps(snps, 25 25  \item{name}{If provided, the name to give the database of SNPs. If not 26 26  provided, defauts to the \code{snps} argument.} 27 27  \item{create}{If the directory provided in the \code{directory} 28 - argument does not exist, create it.} 29 - } 28 + argument does not exist, create it.} 29 + \item{...}{Additional arguments to be passed to the SNPs 30 + replacement method.} 31 +} 30 32   31 33  \section{Accessors}{ 32 34  \describe{ ... ... @@ -36,8 +38,7 @@ Objects can be created by calls of the form \code{GmapSnps(snps, 36 38  this \code{GmapSnps} object.} 37 39  } 38 40  } 39 - 40 -  41 +  41 42  \section{Methods}{ 42 43  \describe{ 43 44  \item{directory}{\code{signature(x = "GmapSnps")}: ... }

#### exporting GmapSnps and GmapSnpDirectory

 ... ... @@ -3,6 +3,7 @@ 3 3  \docType{class} 4 4  \alias{GmapSnps-class} 5 5  \alias{directory,GmapSnps-method} 6 +\alias{GmapSnps} 6 7   7 8  \title{Class \code{"GmapSnps"}} 8 9  \description{ ... ... @@ -14,6 +15,29 @@ 14 15  Objects can be created by calls of the form \code{GmapSnps(snps, 15 16  directory, name, create)}. 16 17  } 18 + 19 +\usage{GmapSnps(snps, directory, name = snps, create = FALSE, ...)} 20 + 21 +\arguments{ 22 + \item{snps}{A path to a VCF file} 23 + \item{directory}{The directory to create the IIT files used by GMAP 24 + and GSNAP} 25 + \item{name}{If provided, the name to give the database of SNPs. If not 26 + provided, defauts to the \code{snps} argument.} 27 + \item{create}{If the directory provided in the \code{directory} 28 + argument does not exist, create it.} 29 + } 30 +  31 +\section{Accessors}{ 32 + \describe{ 33 + \item{}{\code{name(x)}: returns the name of the \code{GmapSnps} object} 34 + \item{}{\code{directory(x)}: returns the \code{GmapGenomeDirectory} 35 + that is the parent of the directory containing the index files for 36 + this \code{GmapSnps} object.} 37 + } 38 +} 39 + 40 +  17 41  \section{Methods}{ 18 42  \describe{ 19 43  \item{directory}{\code{signature(x = "GmapSnps")}: ... }
 1 1 new file mode 100644 ... ... @@ -0,0 +1,25 @@ 1 +\name{GmapSnps-class} 2 +\Rdversion{1.1} 3 +\docType{class} 4 +\alias{GmapSnps-class} 5 +\alias{directory,GmapSnps-method} 6 + 7 +\title{Class \code{"GmapSnps"}} 8 +\description{ 9 + This class represents a set of SNPs (single nucleotide polymorphisms) 10 + for use with GMAP and GSNAP (typically for SNP-tolerant alignment.) 11 +} 12 +\section{Objects from the Class}{ 13 + ##TODO: doc these args 14 +Objects can be created by calls of the form \code{GmapSnps(snps, 15 + directory, name, create)}. 16 +} 17 +\section{Methods}{ 18 + \describe{ 19 + \item{directory}{\code{signature(x = "GmapSnps")}: ... } 20 + } 21 +} 22 +\author{ 23 + Michael Lawrence 24 +} 25 +\keyword{classes}