[Patchwork-commits] r75 - in pkg/patchworkCG: R man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Jan 25 16:58:39 CET 2012
Author: sebastian_d
Date: 2012-01-25 16:58:39 +0100 (Wed, 25 Jan 2012)
New Revision: 75
Modified:
pkg/patchworkCG/R/patchwork.CG.r
pkg/patchworkCG/man/CG_Ka_check.Rd
pkg/patchworkCG/man/patchwork.CG.Rd
pkg/patchworkCG/man/patchwork.CGCNV.Rd
Log:
Added 3 plots to a folder in patchworkCG so people can compare and see what it could look like. Added example text to patchwork.CGCNV and patchwork.CG
Modified: pkg/patchworkCG/R/patchwork.CG.r
===================================================================
--- pkg/patchworkCG/R/patchwork.CG.r 2012-01-25 13:53:13 UTC (rev 74)
+++ pkg/patchworkCG/R/patchwork.CG.r 2012-01-25 15:58:39 UTC (rev 75)
@@ -114,7 +114,7 @@
}
skip_dc = i + 1
- cat("\n","Reading files: \n",mv,"\n",sm,"\n",dc,"\n")
+ cat("Reading files: \n",mv,"\n",sm,"\n",dc,"\n")
#Read mastervarbeta file in ASM folder
mastervar = read.table(masterVarBeta,
sep="\t",
@@ -173,7 +173,7 @@
skip_dc = i + 1
- cat("\n","Reading files from ASM folder \n")
+ cat("Reading files from ASM folder \n")
#Read mastervarbeta file in ASM folder
mastervar = read.table(paste(path,"/",mastervar_,sep=""),
Modified: pkg/patchworkCG/man/CG_Ka_check.Rd
===================================================================
--- pkg/patchworkCG/man/CG_Ka_check.Rd 2012-01-25 13:53:13 UTC (rev 74)
+++ pkg/patchworkCG/man/CG_Ka_check.Rd 2012-01-25 15:58:39 UTC (rev 75)
@@ -99,13 +99,10 @@
\code{\link{patchwork.CGCNV}}
}
-%\examples{
-%##---- Should be DIRECTLY executable !! ----
-%##-- ==> Define data, use random,
-%##-- or do help(data=index) for the standard data sets.
-%Run examples of karyotype stuff. or not, maybe just point back to CNA.
-%}
+%%\examples{
+%%}
+
% Add one or more standard keywords, see file 'KEYWORDS' in the
% R documentation directory.
%\keyword{ ~kwd1 }
Modified: pkg/patchworkCG/man/patchwork.CG.Rd
===================================================================
--- pkg/patchworkCG/man/patchwork.CG.Rd 2012-01-25 13:53:13 UTC (rev 74)
+++ pkg/patchworkCG/man/patchwork.CG.Rd 2012-01-25 15:58:39 UTC (rev 75)
@@ -14,7 +14,9 @@
}
\usage{
-patchwork.CG(path,name='CG_sample_',manual_file_input=FALSE,masterVarBeta=NULL,somaticCnvSegments=NULL,depthOfCoverage=NULL)
+patchwork.CG(path,name='CG_sample_',manual_file_input=FALSE,
+ masterVarBeta=NULL,somaticCnvSegments=NULL,
+ depthOfCoverage=NULL)
}
\arguments{
@@ -91,13 +93,67 @@
%% ~~objects to See Also as \code{\link{help}}, ~~~
%}
-%\examples{
-%##---- Should be DIRECTLY executable !! ----
-%##-- ==> Define data, use random,
-%##-- or do help(data=index) for the standard data sets.
-%Run examples of karyotype stuff. or not, maybe just point back to CNA.
-%}
+\examples{
+\dontrun{
+#Load patchworkCG
+>library(patchworkCG)
+
+#An example of running patchwork.CG. Note that the path is to the ASM folder
+#of the default CompleteGenomics File structure.
+>patchwork.CG(path="Data/HCC2218/GS00258-DNA_B03/GS00258-DNA_B03/ASM",
+ name="HCC2218_")
+
+Reading files from ASM folder
+File input complete
+Performing calculations
+Calculations complete
+Saving objects to CG.Rdata
+Initiating Plotting
+Plotting Complete
+patchwork.CG Complete
+Please read documentation on running patchwork.CGCNV
+
+#The values used to generate the plots are saved in three objects,
+#mastervar,segs and depcov, and can be viewed loading CG.Rdata.
+>load("CG.Rdata")
+
+> head(mastervar)
+ chr begin end vartype ref_count tot_count ref_countN tot_countN
+876 chr1 46669 46670 snp 1 1 2 3
+912 chr1 49313 49315 sub 69 129 71 123
+1030 chr1 55387 55388 snp 64 211 78 247
+1042 chr1 55815 55816 snp 5 12 3 10
+1054 chr1 56484 56485 snp 0 11 2 6
+1082 chr1 57989 57990 snp 58 187 56 177
+ mut_count max min ratio
+876 0 1 0 0.01635786
+912 60 69 60 2.11016381
+1030 147 147 64 3.45150825
+1042 7 7 5 0.19629431
+1054 11 11 0 0.17993645
+1082 129 129 58 3.05891963
+
+> head(segs)
+ chr start end avgnormcov relcov ratio snvs ai
+1 chr1 10000 177417 88.2 1.36 1.0434479 42 0.5449591
+2 chr1 227417 267719 88.2 1.36 1.0434479 0 0.0000000
+3 chr1 317719 471368 88.2 1.36 1.0434479 2 1.0000000
+4 chr1 521368 600000 61.4 0.95 0.8015226 1 1.0000000
+5 chr1 600000 2634220 93.9 1.45 1.0965535 895 0.6904948
+6 chr1 2684220 3845268 93.9 1.45 1.0965535 570 0.8107859
+
+> head(depcov)
+ chr begin end avgnormcov ratio
+1 chr1 10000 100000 94.8 1.0897044
+2 chr1 100000 177417 102.9 1.1622234
+3 chr1 227417 267719 124.4 1.3547120
+4 chr1 317719 400000 99.5 1.1317833
+5 chr1 400000 471368 83.9 0.9921172
+6 chr1 521368 600000 70.1 0.8685663
+}
+}
+
% Add one or more standard keywords, see file 'KEYWORDS' in the
% R documentation directory.
%\keyword{ ~kwd1 }
Modified: pkg/patchworkCG/man/patchwork.CGCNV.Rd
===================================================================
--- pkg/patchworkCG/man/patchwork.CGCNV.Rd 2012-01-25 13:53:13 UTC (rev 74)
+++ pkg/patchworkCG/man/patchwork.CGCNV.Rd 2012-01-25 15:58:39 UTC (rev 75)
@@ -18,7 +18,8 @@
}
\usage{
-patchwork.CGCNV(cn2,delta,het,hom,maxCn=8,ceiling=1,name="CGCNV_",CGfile=NULL)
+patchwork.CGCNV(cn2,delta,het,hom,maxCn=8,ceiling=1,name="CGCNV_",
+ CGfile=NULL)
}
\arguments{
@@ -52,10 +53,10 @@
}
\details{
-1. Run the patchwork.CG correctly. This will generate CG.Rdata.
-2. View your plots and decide the correct parameters for the other arguments of this function.
-3. Make sure CG.Rdata is in your working directory.
-4. Run the function.
+1. Run the patchwork.CG correctly. This will generate CG.Rdata. \cr
+2. View your plots and decide the correct parameters for the other arguments of this function. \cr
+3. Make sure CG.Rdata is in your working directory. \cr
+4. Run the function. \cr
}
%\value{
@@ -85,13 +86,79 @@
\code{\link{subfunctions_CGCNV}}
}
-%\examples{
-%##---- Should be DIRECTLY executable !! ----
-%##-- ==> Define data, use random,
-%##-- or do help(data=index) for the standard data sets.
-%Run examples of karyotype stuff. or not, maybe just point back to CNA.
-%}
+\examples{
+\dontrun{
+>library(patchwork.CG)
+#With CG.Rdata in working directory. Values for parameters estimated from
+#HCC2218 chromosome 1.
+#See plot patchworkCG/example_plots/HCC2218_KaCh_chr1.png
+>patchwork.CGCNV(cn2=0.85,delta=0.35,het=0.25,hom=0.95,name="HCC2218_")
+
+#Pointing to location of CG.Rdata file
+>patchwork.CGCNV(cn2=0.85,delta=0.35,het=0.25,hom=0.95,name="HCC2218_",
+ CGfile="path/to/CG.Rdata")
+
+#Load the objects generated from patchwork.CGCNV
+#For comparison purposes only
+>load("CGCNV.Rdata")
+
+> head(ai)
+$cn2m1
+[1] 0.2460513
+
+$cn2m0
+[1] 0.95
+
+$cn1m0
+[1] 0.9690196
+
+$cn0m0
+[1] NA
+
+$cn3m1
+[1] 0.2677295
+
+$cn3m0
+[1] 0.9671712
+
+> head(int)
+$cn2
+[1] 0.85
+
+$cn1
+[1] 0.5
+
+$cn0
+[1] 0.15
+
+$cn3
+[1] 1.2
+
+$cn4
+[1] 1.55
+
+$cn5
+[1] 1.9
+
+> head(regions)
+ chr start end avgnormcov relcov ratio snvs ai np Cn mCn
+1 chr1 10000 177417 79.0 1.05 0.9660335 24 0.5531915 17 2 1
+2 chr1 227417 267719 79.0 1.05 0.9660335 2 0.3243243 4 2 1
+3 chr1 317719 471368 79.0 1.05 0.9660335 2 0.7826087 15 2 0
+4 chr1 521368 600000 170.8 2.26 2.0792721 2 0.1944444 8 6 3
+5 chr1 600000 700000 74.6 0.99 0.9108316 2 0.5333333 10 2 1
+6 chr1 700000 900000 51.9 0.69 0.6348220 109 0.4960325 20 1 0
+ fullCN
+1 cn2m1
+2 cn2m1
+3 cn2m0
+4 cn6m3
+5 cn2m1
+6 cn1m0
+}
+}
+
% Add one or more standard keywords, see file 'KEYWORDS' in the
% R documentation directory.
%\keyword{ ~kwd1 }
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