[Patchwork-commits] r59 - in pkg: . patchworkData patchworkData/data patchworkData/inst patchworkData/inst/extdata patchworkData/man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu Dec 15 14:15:09 CET 2011
Author: sebastian_d
Date: 2011-12-15 14:15:08 +0100 (Thu, 15 Dec 2011)
New Revision: 59
Added:
pkg/patchworkData/
pkg/patchworkData/DESCRIPTION
pkg/patchworkData/NAMESPACE
pkg/patchworkData/data/
pkg/patchworkData/data/commonSnps132.RData
pkg/patchworkData/data/datalist
pkg/patchworkData/data/datasolexa.RData
pkg/patchworkData/data/datasolid.RData
pkg/patchworkData/data/ideogram.RData
pkg/patchworkData/inst/
pkg/patchworkData/inst/extdata/
pkg/patchworkData/inst/extdata/chr1.mark.rds
pkg/patchworkData/inst/extdata/chr10.mark.rds
pkg/patchworkData/inst/extdata/chr11.mark.rds
pkg/patchworkData/inst/extdata/chr12.mark.rds
pkg/patchworkData/inst/extdata/chr13.mark.rds
pkg/patchworkData/inst/extdata/chr14.mark.rds
pkg/patchworkData/inst/extdata/chr15.mark.rds
pkg/patchworkData/inst/extdata/chr16.mark.rds
pkg/patchworkData/inst/extdata/chr17.mark.rds
pkg/patchworkData/inst/extdata/chr18.mark.rds
pkg/patchworkData/inst/extdata/chr19.mark.rds
pkg/patchworkData/inst/extdata/chr2.mark.rds
pkg/patchworkData/inst/extdata/chr20.mark.rds
pkg/patchworkData/inst/extdata/chr21.mark.rds
pkg/patchworkData/inst/extdata/chr22.mark.rds
pkg/patchworkData/inst/extdata/chr3.mark.rds
pkg/patchworkData/inst/extdata/chr4.mark.rds
pkg/patchworkData/inst/extdata/chr5.mark.rds
pkg/patchworkData/inst/extdata/chr6.mark.rds
pkg/patchworkData/inst/extdata/chr7.mark.rds
pkg/patchworkData/inst/extdata/chr8.mark.rds
pkg/patchworkData/inst/extdata/chr9.mark.rds
pkg/patchworkData/inst/extdata/chrX.mark.rds
pkg/patchworkData/inst/extdata/chrY.mark.rds
pkg/patchworkData/man/
pkg/patchworkData/man/commonSnps132.Rd
pkg/patchworkData/man/datasolexa.Rd
pkg/patchworkData/man/datasolid.Rd
pkg/patchworkData/man/ideogram.Rd
Log:
adding
Added: pkg/patchworkData/DESCRIPTION
===================================================================
--- pkg/patchworkData/DESCRIPTION (rev 0)
+++ pkg/patchworkData/DESCRIPTION 2011-12-15 13:15:08 UTC (rev 59)
@@ -0,0 +1,14 @@
+Package: patchworkData
+Type: Package
+Title: Data for patchwork package.
+Version: 2.0
+Date: 2011-10-13
+Author: Markus Rasmussen, Sebastian DiLorenzo
+Maintainer: Markus Rasmussen <Markus.Rasmussen at medsci.uu.se>
+Description: The data needed to perform patchwork functions.
+License: GPL-2
+#LazyLoad: no
+#LazyData: yes
+Depends: R (>= 2.10)
+Packaged: 2011-12-15 08:39:57 UTC; S_D
+Namespace: auto
Added: pkg/patchworkData/NAMESPACE
===================================================================
--- pkg/patchworkData/NAMESPACE (rev 0)
+++ pkg/patchworkData/NAMESPACE 2011-12-15 13:15:08 UTC (rev 59)
@@ -0,0 +1,5 @@
+# Default NAMESPACE created by R
+# Remove the previous line if you edit this file
+
+# Export all names
+exportPattern(".")
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===================================================================
--- pkg/patchworkData/data/datalist (rev 0)
+++ pkg/patchworkData/data/datalist 2011-12-15 13:15:08 UTC (rev 59)
@@ -0,0 +1,4 @@
+commonSnps132: dbSnp
+datasolexa
+datasolid
+ideogram
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Added: pkg/patchworkData/man/commonSnps132.Rd
===================================================================
--- pkg/patchworkData/man/commonSnps132.Rd (rev 0)
+++ pkg/patchworkData/man/commonSnps132.Rd 2011-12-15 13:15:08 UTC (rev 59)
@@ -0,0 +1,41 @@
+\name{commonSnps132}
+\alias{commonSnps132}
+\alias{dbSnp}
+\docType{data}
+
+\title{
+Chromosome SNP start and stop positions.
+}
+
+\description{
+Chromosome SNP start and stop positions.
+}
+
+
+\usage{commonSnps132}
+
+\format{
+ A data frame with the following 3 variables.
+ \describe{
+ \item{chrom}{Which chromosome}
+ \item{chromStart}{Start of SNP}
+ \item{chromEnd}{End of SNP}
+ }
+}
+
+\details{
+SNP data version 132.
+}
+
+%\source{
+% \url{http://www.}
+%}
+
+\seealso{
+ The function \code{\link[patchwork]{patchwork.alleledata}} uses this data.
+}
+
+%\examples{
+%}
+
+%\keyword{datasets}
\ No newline at end of file
Added: pkg/patchworkData/man/datasolexa.Rd
===================================================================
--- pkg/patchworkData/man/datasolexa.Rd (rev 0)
+++ pkg/patchworkData/man/datasolexa.Rd 2011-12-15 13:15:08 UTC (rev 59)
@@ -0,0 +1,40 @@
+\name{datasolexa}
+\alias{datasolexa}
+\docType{data}
+
+\title{
+Reference file for Solexa(Illumina) sequenced data.
+}
+
+\description{
+Reference file for Solexa(Illumina) sequenced data.
+}
+
+
+\usage{datasolexa}
+
+\format{
+ A data frame with the following 3 columns.
+ \describe{
+ \item{chr}{Which chromosome}
+ \item{pos}{Position on chromosome}
+ \item{norm_mean}{Mean of normalized coverage}
+ }
+}
+
+\details{
+Reference file for Solexa(Illumina) sequenced data.
+}
+
+%\source{
+% \url{http://www.}
+%}
+
+\seealso{
+ The function \code{\link[patchwork]{patchwork.applyref}} uses this data.
+}
+
+%\examples{
+%}
+
+%\keyword{datasets}
\ No newline at end of file
Added: pkg/patchworkData/man/datasolid.Rd
===================================================================
--- pkg/patchworkData/man/datasolid.Rd (rev 0)
+++ pkg/patchworkData/man/datasolid.Rd 2011-12-15 13:15:08 UTC (rev 59)
@@ -0,0 +1,40 @@
+\name{datasolid}
+\alias{datasolid}
+\docType{data}
+
+\title{
+Reference file for SOLiD sequenced data.
+}
+
+\description{
+Reference file for SOLiD sequenced data.
+}
+
+
+\usage{datasolid}
+
+\format{
+ A data frame with the following 3 columns.
+ \describe{
+ \item{chr}{Which chromosome}
+ \item{pos}{Position on chromosome}
+ \item{norm_mean}{Mean of normalized coverage}
+ }
+}
+
+\details{
+Reference file for SOLiD sequenced data.
+}
+
+%\source{
+% \url{http://www.}
+%}
+
+\seealso{
+ The function \code{\link[patchwork]{patchwork.applyref}} uses this data.
+}
+
+%\examples{
+%}
+
+%\keyword{datasets}
\ No newline at end of file
Added: pkg/patchworkData/man/ideogram.Rd
===================================================================
--- pkg/patchworkData/man/ideogram.Rd (rev 0)
+++ pkg/patchworkData/man/ideogram.Rd 2011-12-15 13:15:08 UTC (rev 59)
@@ -0,0 +1,44 @@
+\name{ideogram}
+\alias{ideogram}
+\docType{data}
+
+\title{
+Ideogram data for the chromosomes.
+}
+
+\description{
+Ideogram data for the chromosomes.
+}
+
+
+\usage{ideogram}
+
+\format{
+ A data frame with the following 6 variables.
+ \describe{
+ \item{chr}{Which chromosome}
+ \item{length}{Length of chromosome}
+ \item{start}{Start of centromere}
+ \item{mid}{Middle of centromere}
+ \item{end}{End of centromere}
+ \item{c}{Easy integer to chromosome number}
+ }
+}
+
+\details{
+Ideogram data for the chromosomes. Used in many functions.
+}
+
+%\source{
+% \url{http://www.}
+%}
+
+\seealso{
+ The function \code{\link[patchwork]{patchwork.CNA}}, and other functions withing the package,
+ uses this data.
+}
+
+%\examples{
+%}
+
+%\keyword{datasets}
\ No newline at end of file
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