Last data update: 2014.03.03
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snapCGH
Package: snapCGH
Title: Segmentation, normalisation and processing of aCGH data.
Version: 1.42.0
Date: 2009-10-08
Author: Mike L. Smith, John C. Marioni, Steven McKinney, Thomas
Hardcastle, Natalie P. Thorne
Description: Methods for segmenting, normalising and processing aCGH
data; including plotting functions for visualising raw and
segmented data for individual and multiple arrays.
Maintainer: John Marioni <marioni@uchicago.edu>
Depends: limma, DNAcopy, methods
Imports: aCGH, cluster, DNAcopy, GLAD, graphics, grDevices, limma,
methods, stats, tilingArray, utils
License: GPL
biocViews: Microarray, CopyNumberVariation, TwoChannel, Preprocessing
NeedsCompilation: yes
Packaged: 2016-05-04 02:49:21 UTC; biocbuild
● BiocViews: CopyNumberVariation, Microarray, Preprocessing, TwoChannel
●
0 images,
35 functions,
8 datasets
●
Reverse Depends: 0
Install log
* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'snapCGH' ...
** libs
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c optimizer.c -o optimizer.o
gcc -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o snapCGH.so optimizer.o -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/snapCGH/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
converting help for package 'snapCGH'
finding HTML links ... done
IDProbes html
LargeDataObject html
SegList html
Viterbi.five html
Viterbi.four html
Viterbi.three html
Viterbi.two html
cbind html
chrominfo.Mb html
compareSegmentations html
convert.output html
dim html
dimnames html
filter html
find.param.five html
find.param.four html
find.param.one html
find.param.three html
find.param.two html
findBreakPoints html
fit.model html
genomePlot html
heatmapGenome html
imputeMissingValues html
log2ratios html
mergeStates html
non.zero.length.distr.non.tiled html
non.zero.length.distr.tiled html
plotSegmentedGenome html
processCGH html
read.clonesinfo html
readPositionalInfo html
removeByWeights html
runBioHMM html
runDNAcopy html
runGLAD html
runHMM html
runTilingArray html
sim.structure html
zero.length.distr.non.tiled html
zero.length.distr.tiled html
zoomChromosome html
zoomGenome html
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (snapCGH)
Making 'packages.html' ... done
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