#### cleaned up a few of the classes. defined new class called CNSet to take the place of CrlmmSet

Rob Scharp authored on 19/11/2009 14:59:04
Showing 1 changed files
 1 1 deleted file mode 100644 ... ... @@ -1,58 +0,0 @@ 1 -\name{methods-eSet} 2 -\alias{chromosome} 3 -\alias{chromosome,eSet-method} 4 -\alias{cnIndex} 5 -\alias{cnIndex,eSet-method} 6 -\alias{position} 7 -\alias{position,eSet-method} 8 -\alias{snpIndex} 9 -\alias{snpIndex,eSet-method} 10 - 11 -\title{Methods for eSet derivatives} 12 - 13 -\description{ 14 - \code{chromosome} return the chromosome number for SNP and NP probes. 15 -  16 - \code{cnIndex, ...} return the row indices of copy number probes. 17 - 18 - \code{position} return the physical position of the SNP or the 19 - physical position for the first index of the NP probe. 20 -  21 - \code{snpIndex, ...} return the row indices of polymorphic loci. 22 - 23 -} 24 - 25 -\usage{ 26 - 27 - chromosome(object) 28 - cnIndex(object, ...) 29 - position(object) 30 - snpIndex(object, ...) 31 - 32 -} 33 - 34 -\arguments{ 35 -  36 - \item{object}{Any object extending eSet (ABset, CopyNumberSet, 37 - CrlmmSetList, SnpSet} 38 - 39 - \item{\dots}{Usually the character string indicating annotation package.} 40 - 41 -} 42 - 43 -\value{ 44 - 45 - Vector of indices. 46 - 47 -} 48 - 49 -\seealso{ 50 - 51 - \code{"\linkS4class{ABset}"} 52 - \code{"\linkS4class{CopyNumberSet}"} 53 - \code{"\linkS4class{CrlmmSetList}"} 54 -  55 -} 56 -  57 - 58 -\keyword{manip} 59 0 \ No newline at end of file

#### changes to crlmmWrapper. updated vignettes in inst/scripts.

Rob Scharp authored on 04/10/2009 02:37:32
Showing 1 changed files
 ... ... @@ -1,24 +1,32 @@ 1 1  \name{methods-eSet} 2 +\alias{chromosome} 3 +\alias{chromosome,eSet-method} 2 4  \alias{cnIndex} 3 5  \alias{cnIndex,eSet-method} 6 +\alias{position} 7 +\alias{position,eSet-method} 4 8  \alias{snpIndex} 5 9  \alias{snpIndex,eSet-method} 6 10   7 - 8 11  \title{Methods for eSet derivatives} 9 12   10 13  \description{ 14 + \code{chromosome} return the chromosome number for SNP and NP probes. 15 +  16 + \code{cnIndex, ...} return the row indices of copy number probes. 11 17   18 + \code{position} return the physical position of the SNP or the 19 + physical position for the first index of the NP probe. 20 +  12 21  \code{snpIndex, ...} return the row indices of polymorphic loci. 13 22   14 - \code{cnIndex, ...} return the row indices of copy number probes. 15 - 16 23  } 17 24   18 25  \usage{ 19 26   27 + chromosome(object) 20 28  cnIndex(object, ...) 21 - 29 + position(object) 22 30  snpIndex(object, ...) 23 31   24 32  }

#### changes to vignette. removed crlmmIlluminaWrapper function. added boxplot method

Rob Scharp authored on 14/08/2009 14:14:25
Showing 1 changed files
 ... ... @@ -17,9 +17,9 @@ 17 17   18 18  \usage{ 19 19   20 - cnIndex(object, cdfName) 20 + cnIndex(object, ...) 21 21   22 - snpIndex(object, cdfName) 22 + snpIndex(object, ...) 23 23   24 24  } 25 25   ... ... @@ -28,7 +28,7 @@ 28 28  \item{object}{Any object extending eSet (ABset, CopyNumberSet, 29 29  CrlmmSetList, SnpSet} 30 30   31 - \item{cdfName}{Character string indicating annotation package.} 31 + \item{\dots}{Usually the character string indicating annotation package.} 32 32   33 33  } 34 34 

#### several updates to vignette, documentation, and copy number for illumina.

 ... ... @@ -9,17 +9,17 @@ 9 9   10 10  \description{ 11 11   12 - \code{snpIndex} return the row indices of polymorphic loci. 12 + \code{snpIndex, ...} return the row indices of polymorphic loci. 13 13   14 - \code{cnIndex} return the row indices of copy number probes. 14 + \code{cnIndex, ...} return the row indices of copy number probes. 15 15   16 16  } 17 17   18 18  \usage{ 19 19   20 - cnIndex(object) 20 + cnIndex(object, cdfName) 21 21   22 - snpIndex(object) 22 + snpIndex(object, cdfName) 23 23   24 24  } 25 25   ... ... @@ -28,6 +28,8 @@ 28 28  \item{object}{Any object extending eSet (ABset, CopyNumberSet, 29 29  CrlmmSetList, SnpSet} 30 30   31 + \item{cdfName}{Character string indicating annotation package.} 32 + 31 33  } 32 34   33 35  \value{
 1 1 new file mode 100644 ... ... @@ -0,0 +1,48 @@ 1 +\name{methods-eSet} 2 +\alias{cnIndex} 3 +\alias{cnIndex,eSet-method} 4 +\alias{snpIndex} 5 +\alias{snpIndex,eSet-method} 6 + 7 + 8 +\title{Methods for eSet derivatives} 9 + 10 +\description{ 11 + 12 + \code{snpIndex} return the row indices of polymorphic loci. 13 + 14 + \code{cnIndex} return the row indices of copy number probes. 15 + 16 +} 17 + 18 +\usage{ 19 + 20 + cnIndex(object) 21 + 22 + snpIndex(object) 23 + 24 +} 25 + 26 +\arguments{ 27 +  28 + \item{object}{Any object extending eSet (ABset, CopyNumberSet, 29 + CrlmmSetList, SnpSet} 30 + 31 +} 32 + 33 +\value{ 34 + 35 + Vector of indices. 36 + 37 +} 38 + 39 +\seealso{ 40 + 41 + \code{"\linkS4class{ABset}"} 42 + \code{"\linkS4class{CopyNumberSet}"} 43 + \code{"\linkS4class{CrlmmSetList}"} 44 +  45 +} 46 +  47 + 48 +\keyword{manip} 0 49 \ No newline at end of file