[Patchwork-commits] r33 - in pkg/patchwork: . R man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Nov 30 15:17:15 CET 2011
Author: sebastian_d
Date: 2011-11-30 15:17:13 +0100 (Wed, 30 Nov 2011)
New Revision: 33
Modified:
pkg/patchwork/DESCRIPTION
pkg/patchwork/R/karyotype_chromsCN.r
pkg/patchwork/R/patchwork.CNA.r
pkg/patchwork/man/datasolexa.Rd
pkg/patchwork/man/datasolid.Rd
pkg/patchwork/man/karyotype.Rd
pkg/patchwork/man/karyotype_chroms.Rd
pkg/patchwork/man/patchwork.CNA.Rd
pkg/patchwork/man/patchwork.GCNorm.Rd
pkg/patchwork/man/patchwork.Medians_n_AI.Rd
pkg/patchwork/man/patchwork.alleledata.Rd
pkg/patchwork/man/patchwork.applyref.Rd
pkg/patchwork/man/patchwork.createreference.Rd
pkg/patchwork/man/patchwork.findCNs.Rd
pkg/patchwork/man/patchwork.segment.Rd
pkg/patchwork/man/patchwork.smoothing.Rd
pkg/patchwork/man/subfunctions_findCNs.Rd
Log:
Last commit pre attempting to create patchworkData
Modified: pkg/patchwork/DESCRIPTION
===================================================================
--- pkg/patchwork/DESCRIPTION 2011-11-29 11:04:59 UTC (rev 32)
+++ pkg/patchwork/DESCRIPTION 2011-11-30 14:17:13 UTC (rev 33)
@@ -1,7 +1,7 @@
Package: patchwork
Type: Package
Title: Allele-specific Copy Number Analysis of Whole genome data
-Version: 1.0
+Version: 1.9
Date: 2011-10-13
Author: Markus Rasmussen, Sebastian DiLorenzo
Maintainer: Markus Rasmussen <Markus.Rasmussen at medsci.uu.se>
@@ -9,5 +9,5 @@
License: GPL-2
LazyLoad: no
#LazyData: yes
-Depends: DNAcopy
-Imports: DNAcopy
+Depends: DNAcopy, patchworkData
+Imports: DNAcopy, patchworkData
Modified: pkg/patchwork/R/karyotype_chromsCN.r
===================================================================
--- pkg/patchwork/R/karyotype_chromsCN.r 2011-11-29 11:04:59 UTC (rev 32)
+++ pkg/patchwork/R/karyotype_chromsCN.r 2011-11-30 14:17:13 UTC (rev 33)
@@ -11,6 +11,7 @@
# so it will work independent of chr field name.
chroms = as.character(unique(schr))
+ chroms = chroms[chroms != chroms[grep("M",chroms)]]
ideogram$chr = chroms
Modified: pkg/patchwork/R/patchwork.CNA.r
===================================================================
--- pkg/patchwork/R/patchwork.CNA.r 2011-11-29 11:04:59 UTC (rev 32)
+++ pkg/patchwork/R/patchwork.CNA.r 2011-11-30 14:17:13 UTC (rev 33)
@@ -25,6 +25,7 @@
}
chroms=as.character(unique(alf$achr))
+ chroms = chroms[chroms != chroms[grep("M",chroms)]]
## Read coverage data. If already done, will load "data.Rdata" instead.
data=NULL
Modified: pkg/patchwork/man/datasolexa.Rd
===================================================================
--- pkg/patchwork/man/datasolexa.Rd 2011-11-29 11:04:59 UTC (rev 32)
+++ pkg/patchwork/man/datasolexa.Rd 2011-11-30 14:17:13 UTC (rev 33)
@@ -26,9 +26,9 @@
Reference file for Solexa(Illumina) sequenced data.
}
-%\source{
-% \url{http://www.}
-%}
+\source{
+ \url{http://www.ncbi.nlm.nih.gov/} , Illumina Genome Analyzer II
+}
\seealso{
The function \code{\link{patchwork.applyref}} uses this data.
Modified: pkg/patchwork/man/datasolid.Rd
===================================================================
--- pkg/patchwork/man/datasolid.Rd 2011-11-29 11:04:59 UTC (rev 32)
+++ pkg/patchwork/man/datasolid.Rd 2011-11-30 14:17:13 UTC (rev 33)
@@ -26,9 +26,9 @@
Reference file for SOLiD sequenced data.
}
-%\source{
-% \url{http://www.}
-%}
+\source{
+ \url{http://www.ncbi.nlm.nih.gov/}, AB SOLiD System 2.0
+}
\seealso{
The function \code{\link{patchwork.applyref}} uses this data.
Modified: pkg/patchwork/man/karyotype.Rd
===================================================================
--- pkg/patchwork/man/karyotype.Rd 2011-11-29 11:04:59 UTC (rev 32)
+++ pkg/patchwork/man/karyotype.Rd 2011-11-30 14:17:13 UTC (rev 33)
@@ -76,7 +76,7 @@
%% ~Make other sections like Warning with \section{Warning }{....} ~
\seealso{
-\code{\link{patchwork.CNA}}
+\code{\link{patchwork.CNA}} \cr
\code{\link{karyotype_chroms}}
}
Modified: pkg/patchwork/man/karyotype_chroms.Rd
===================================================================
--- pkg/patchwork/man/karyotype_chroms.Rd 2011-11-29 11:04:59 UTC (rev 32)
+++ pkg/patchwork/man/karyotype_chroms.Rd 2011-11-30 14:17:13 UTC (rev 33)
@@ -112,7 +112,7 @@
%% ~Make other sections like Warning with \section{Warning }{....} ~
\seealso{
-\code{\link{patchwork.CNA}}
+\code{\link{patchwork.CNA}} \cr
\code{\link{karyotype}}
}
Modified: pkg/patchwork/man/patchwork.CNA.Rd
===================================================================
--- pkg/patchwork/man/patchwork.CNA.Rd 2011-11-29 11:04:59 UTC (rev 32)
+++ pkg/patchwork/man/patchwork.CNA.Rd 2011-11-30 14:17:13 UTC (rev 33)
@@ -52,11 +52,11 @@
Upon completion of the the method you may receive the following warnings:
-Warning messages:
-1: In readChar(con, 5L, useBytes = TRUE) :
- cannot open compressed file 'data.Rdata', probable reason 'No such file or directory'
-2: In readChar(con, 5L, useBytes = TRUE) :
- cannot open compressed file 'pile.alleles.Rdata', probable reason 'No such file or directory'
+Warning messages: \cr
+1: In readChar(con, 5L, useBytes = TRUE) : \cr
+ cannot open compressed file 'data.Rdata', probable reason 'No such file or directory' \cr
+2: In readChar(con, 5L, useBytes = TRUE) : \cr
+ cannot open compressed file 'pile.alleles.Rdata', probable reason 'No such file or directory' \cr
This is not unusal, it just means its the first time you've run the patchwork.CNA
function in this directory.
Modified: pkg/patchwork/man/patchwork.GCNorm.Rd
===================================================================
--- pkg/patchwork/man/patchwork.GCNorm.Rd 2011-11-29 11:04:59 UTC (rev 32)
+++ pkg/patchwork/man/patchwork.GCNorm.Rd 2011-11-30 14:17:13 UTC (rev 33)
@@ -4,11 +4,11 @@
\title{
-patchworks gc normalizing function
+patchwork GC normalizing function
}
\description{
-description
+Performs GC normalization on the data,
}
\usage{
@@ -22,7 +22,7 @@
}
\details{
-Details
+First performs normalization in a 200 base window and then on a 1000 base window.
}
%\value{
@@ -47,9 +47,9 @@
%% ~Make other sections like Warning with \section{Warning }{....} ~
-%\seealso{
-%% ~~objects to See Also as \code{\link{help}}, ~~~
-%}
+\seealso{
+\code{\link{patchwork.CNA}}
+}
%\examples{
%##---- Should be DIRECTLY executable !! ----
Modified: pkg/patchwork/man/patchwork.Medians_n_AI.Rd
===================================================================
--- pkg/patchwork/man/patchwork.Medians_n_AI.Rd 2011-11-29 11:04:59 UTC (rev 32)
+++ pkg/patchwork/man/patchwork.Medians_n_AI.Rd 2011-11-30 14:17:13 UTC (rev 33)
@@ -53,9 +53,9 @@
%% ~Make other sections like Warning with \section{Warning }{....} ~
-%\seealso{
-%% ~~objects to See Also as \code{\link{help}}, ~~~
-%}
+\seealso{
+\code{\link{patchwork.CNA}}
+}
%\examples{
%##---- Should be DIRECTLY executable !! ----
Modified: pkg/patchwork/man/patchwork.alleledata.Rd
===================================================================
--- pkg/patchwork/man/patchwork.alleledata.Rd 2011-11-29 11:04:59 UTC (rev 32)
+++ pkg/patchwork/man/patchwork.alleledata.Rd 2011-11-30 14:17:13 UTC (rev 33)
@@ -8,7 +8,9 @@
}
\description{
-description
+Loads the data object commonSnps132.RData and uses the perl script, included in package,
+pile2alleles.pl to generate pile.alleles in your working directory. This will be read into R
+as the alf object and then the file pile.alleles removed.
}
\usage{
@@ -22,7 +24,9 @@
}
\details{
-Details
+Uses SNP data to calculate allele frequencies of the sample. Currently uses SNP132.
+
+patchwork.alleledata is a subfunction to patchwork.CNA.
}
%\value{
@@ -47,9 +51,9 @@
%% ~Make other sections like Warning with \section{Warning }{....} ~
-%\seealso{
-%% ~~objects to See Also as \code{\link{help}}, ~~~
-%}
+\seealso{
+\code{\link{patchwork.CNA}}
+}
%\examples{
%##---- Should be DIRECTLY executable !! ----
Modified: pkg/patchwork/man/patchwork.applyref.Rd
===================================================================
--- pkg/patchwork/man/patchwork.applyref.Rd 2011-11-29 11:04:59 UTC (rev 32)
+++ pkg/patchwork/man/patchwork.applyref.Rd 2011-11-30 14:17:13 UTC (rev 33)
@@ -53,7 +53,7 @@
%% ~Make other sections like Warning with \section{Warning }{....} ~
\seealso{
-\code{\link{patchwork.CNA}}
+\code{\link{patchwork.CNA}} \cr
\code{\link{patchwork.createreference}}
}
Modified: pkg/patchwork/man/patchwork.createreference.Rd
===================================================================
--- pkg/patchwork/man/patchwork.createreference.Rd 2011-11-29 11:04:59 UTC (rev 32)
+++ pkg/patchwork/man/patchwork.createreference.Rd 2011-11-30 14:17:13 UTC (rev 33)
@@ -63,9 +63,9 @@
%\code{\link{help}}
\seealso{
-\code{\link{patchwork.CNA}}
-\code{\link{patchwork.readChroms}}
-\code{\link{patchwork.applyref}}
+\code{\link{patchwork.CNA}} \cr
+\code{\link{patchwork.readChroms}} \cr
+\code{\link{patchwork.applyref}} \cr
\code{\link{patchwork.GCNorm}}
}
Modified: pkg/patchwork/man/patchwork.findCNs.Rd
===================================================================
--- pkg/patchwork/man/patchwork.findCNs.Rd 2011-11-29 11:04:59 UTC (rev 32)
+++ pkg/patchwork/man/patchwork.findCNs.Rd 2011-11-30 14:17:13 UTC (rev 33)
@@ -72,7 +72,7 @@
%% ~Make other sections like Warning with \section{Warning }{....} ~
\seealso{
-\code{\link{patchwork.CNA}}
+\code{\link{patchwork.CNA}} \cr
\code{\link{subfunctions_findCNs}}
}
Modified: pkg/patchwork/man/patchwork.segment.Rd
===================================================================
--- pkg/patchwork/man/patchwork.segment.Rd 2011-11-29 11:04:59 UTC (rev 32)
+++ pkg/patchwork/man/patchwork.segment.Rd 2011-11-30 14:17:13 UTC (rev 33)
@@ -60,8 +60,8 @@
%% ~Make other sections like Warning with \section{Warning }{....} ~
\seealso{
-\code{\link{patchwork.CNA}}
-\code{\link{DNAcopy}}
+\code{\link{patchwork.CNA}} \cr
+\code{\link{DNAcopy}} \cr
\code{\link{segment}}
}
Modified: pkg/patchwork/man/patchwork.smoothing.Rd
===================================================================
--- pkg/patchwork/man/patchwork.smoothing.Rd 2011-11-29 11:04:59 UTC (rev 32)
+++ pkg/patchwork/man/patchwork.smoothing.Rd 2011-11-30 14:17:13 UTC (rev 33)
@@ -8,7 +8,7 @@
}
\description{
-description
+Applies smoothing by averaging kb segments.
}
\usage{
@@ -20,13 +20,13 @@
data object generated after patchwork.GCNorm().
}
\item{chroms}{
- chroms is an object generated from ideogram.RData's ideogram\$chr attribute.
+ chroms is an object generated from pile.alleles.RData's alf\$achr attribute.
}
}
-\details{
-Details
-}
+%\details{
+%Details
+%}
%\value{
%% ~Describe the value returned
@@ -50,9 +50,9 @@
%% ~Make other sections like Warning with \section{Warning }{....} ~
-%\seealso{
-%% ~~objects to See Also as \code{\link{help}}, ~~~
-%}
+\seealso{
+\code{\link{patchwork.CNA}}
+}
%\examples{
%##---- Should be DIRECTLY executable !! ----
Modified: pkg/patchwork/man/subfunctions_findCNs.Rd
===================================================================
--- pkg/patchwork/man/subfunctions_findCNs.Rd 2011-11-29 11:04:59 UTC (rev 32)
+++ pkg/patchwork/man/subfunctions_findCNs.Rd 2011-11-30 14:17:13 UTC (rev 33)
@@ -61,9 +61,9 @@
%% ~Make other sections like Warning with \section{Warning }{....} ~
-%\seealso{
-%% ~~objects to See Also as \code{\link{help}}, ~~~
-%}
+\seealso{
+\code{\link{patchwork.findCNs}}
+}
%\examples{
%##---- Should be DIRECTLY executable !! ----
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