snapCGH: Segmentation, normalisation and processing of aCGH data.

Methods for segmenting, normalising and processing aCGH data; including plotting functions for visualising raw and segmented data for individual and multiple arrays.

AuthorMike L. Smith, John C. Marioni, Steven McKinney, Thomas Hardcastle, Natalie P. Thorne
Date of publicationNone
MaintainerJohn Marioni <marioni@uchicago.edu>
LicenseGPL
Version1.44.0

View on Bioconductor

Man pages

cbind: Combine SegList Objects

chrominfo.Mb: Basic Chromosomal Information for UCSC Human Genome Assembly...

compareSegmentations: Function for comparing segmentation methods to a known truth

convert.output: Converts the output from the simulation to a format which can...

dim: Retrieve the Dimensions of an RGList, MAList or SegList...

dimnames: Retrieve the Dimension Names of an RGList, MAList or SegList...

filter: Filter clones from sample

findBreakPoints: Returns the start and end of segments.

find.param.five: Yields the output in a model with five underlying states

find.param.four: Yields output when there are 4 underlying states

find.param.one: Yields output when there is 1 underlying states

find.param.three: Yields output when there are 3 underlying states

find.param.two: Yields output when there are 2 underlying states

fit.model: Fitting a heterogeneous HMM to the log2 ratios on a...

genomePlot: Plots the genome

heatmapGenome: clustering and heatmap

IDProbes: Interactive version of genomePlot

imputeMissingValues: Imputing log2 ratios

LargeDataObject: Large Data Object - class

log2ratios: Extracting log2 ratios

mergeStates: Function to merge states based on their state means

non.zero.length.distr.non.tiled: Empirical distribution of segment lengths in non-tiled...

non.zero.length.distr.tiled: Empirical distribution of segment lengths in tiled regions...

plotSegmentedGenome: Plots the genome

processCGH: Process data in an MAList

read.clonesinfo: Reading chromsome and positional information about each...

readPositionalInfo: readPositionalInfo

removeByWeights: Remove clones based on a weights matrix

runBioHMM: This function implements the BioHMM

runDNAcopy: Results of segmenting an MAList data object using the DNAcopy...

runGLAD: Results of segmenting an aCGHList data object using the GLAD...

runHMM: A function to fit unsupervised Hidden Markov model

runTilingArray: Results of segmenting an MAList data object using the Picard...

SegList: Segmentation States - class

sim.structure: A function for simulating aCGH data and the corresponding...

Viterbi.five: A scaled Viterbi algorithm for allocating clones to one of...

Viterbi.four: A scaled Viterbi algorithm for allocating clones to one of...

Viterbi.three: A scaled Viterbi algorithm for allocating clones to one of...

Viterbi.two: A scaled Viterbi algorithm for allocating clones to one of...

zero.length.distr.non.tiled: Empirical distribution of segment lengths in non-tiled...

zero.length.distr.tiled: Empirical distribution of segment lengths in tiled regions...

zoomChromosome: Interactive plot of a single chromsome

zoomGenome: Interactive plot of the whole genome

Functions

cbind.SegList Man page
chrominfo.Mb Man page
combine.func Man page
compareBreakPoints Man page
compareSegmentations Man page
convert.output Man page
dim Man page
dim.MAList Man page
dimnames Man page
dimnames.SegList Man page
dimnames,SegList-method Man page
dim.RGList Man page
dim.SegList Man page
dim,SegList-method Man page
filterClones Man page
findBreakPoints Man page
find.param.five Man page
find.param.four Man page
find.param.one Man page
find.param.three Man page
find.param.two Man page
fit.model Man page
floor.func Man page
generate.data Man page
genomePlot Man page
heatmapGenome Man page
IDProbes Man page
imputeMissingValues Man page
LargeDataObject-class Man page
length Man page
length.MAList Man page
length.RGList Man page
length.SegList Man page
length,SegList-method Man page
log2ratios Man page
maPalette Man page
MergeLevels.new Man page
MergeLevels.old Man page
mergeStates Man page
non.zero.length.distr.non.tiled Man page
non.zero.length.distr.tiled Man page
plotChrom Man page
plotSegmentedGenome Man page
plotValChrom Man page
plotvalChrom.func Man page
plotValGenome Man page
print.SegList Man page
processCGH Man page
prop.na Man page
rbind.SegList Man page
read.clonesinfo Man page
readPositionalInfo Man page
removeByWeights Man page
runBioHMM Man page
runDNAcopy Man page
runGLAD Man page
runHomHMM Man page
run.nelder Man page
runTilingArray Man page
sample.names Man page
[.SegList Man page
SegList-class Man page
show,LargeDataObject-method Man page
show,SegList-method Man page
simulateData Man page
states.hmm.func Man page
Viterbi.five Man page
Viterbi.four Man page
Viterbi.three Man page
Viterbi.two Man page
zero.length.distr.non.tiled Man page
zero.length.distr.tiled Man page
zoomChromosome Man page
zoomGenome Man page

Files

snapCGH/DESCRIPTION
snapCGH/NAMESPACE
snapCGH/R
snapCGH/R/IDProbes.R snapCGH/R/MergeStates.R snapCGH/R/Newplotting.R snapCGH/R/SegAnalysis.R snapCGH/R/Viterbi.five.R snapCGH/R/Viterbi.four.R snapCGH/R/Viterbi.three.R snapCGH/R/Viterbi.two.R snapCGH/R/chrominfo.Mb.R snapCGH/R/classes.R snapCGH/R/convert.output.R snapCGH/R/filter.R snapCGH/R/find.param.five.R snapCGH/R/find.param.four.R snapCGH/R/find.param.one.R snapCGH/R/find.param.three.R snapCGH/R/find.param.two.R snapCGH/R/findBreakPoints.R snapCGH/R/fit.model.R snapCGH/R/hmm.R snapCGH/R/misc.R snapCGH/R/processCGH.R snapCGH/R/readPositionalInfo.R snapCGH/R/runBioHMM.R snapCGH/R/runDNAcopy.R snapCGH/R/runGLAD.R snapCGH/R/runTilingArray.R snapCGH/R/simulateData.R snapCGH/R/zoomFunctions.R
snapCGH/build
snapCGH/build/vignette.rds
snapCGH/data
snapCGH/data/non.zero.length.distr.non.tiled.rda
snapCGH/data/non.zero.length.distr.tiled.rda
snapCGH/data/zero.length.distr.non.tiled.rda
snapCGH/data/zero.length.distr.tiled.rda
snapCGH/inst
snapCGH/inst/doc
snapCGH/inst/doc/snapCGHguide.R
snapCGH/inst/doc/snapCGHguide.Rnw
snapCGH/inst/doc/snapCGHguide.pdf
snapCGH/inst/testdata
snapCGH/inst/testdata/10Mbslide28.gpr
snapCGH/inst/testdata/10Mbslide29.gpr
snapCGH/inst/testdata/SpotTypes.txt
snapCGH/inst/testdata/cloneinfo.txt
snapCGH/inst/testdata/targets.txt
snapCGH/man
snapCGH/man/IDProbes.Rd snapCGH/man/LargeDataObject.Rd snapCGH/man/SegList.Rd snapCGH/man/Viterbi.five.Rd snapCGH/man/Viterbi.four.Rd snapCGH/man/Viterbi.three.Rd snapCGH/man/Viterbi.two.Rd snapCGH/man/cbind.Rd snapCGH/man/chrominfo.Mb.Rd snapCGH/man/compareSegmentations.Rd snapCGH/man/convert.output.Rd snapCGH/man/dim.Rd snapCGH/man/dimnames.Rd snapCGH/man/filter.Rd snapCGH/man/find.param.five.Rd snapCGH/man/find.param.four.Rd snapCGH/man/find.param.one.Rd snapCGH/man/find.param.three.Rd snapCGH/man/find.param.two.Rd snapCGH/man/findBreakPoints.Rd snapCGH/man/fit.model.Rd snapCGH/man/genomePlot.Rd snapCGH/man/heatmapGenome.Rd snapCGH/man/imputeMissingValues.Rd snapCGH/man/log2ratios.Rd snapCGH/man/mergeStates.Rd snapCGH/man/non.zero.length.distr.non.tiled.Rd snapCGH/man/non.zero.length.distr.tiled.Rd snapCGH/man/plotSegmentedGenome.Rd snapCGH/man/processCGH.Rd snapCGH/man/read.clonesinfo.Rd snapCGH/man/readPositionalInfo.Rd snapCGH/man/removeByWeights.Rd snapCGH/man/runBioHMM.Rd snapCGH/man/runDNAcopy.Rd snapCGH/man/runGLAD.Rd snapCGH/man/runHMM.Rd snapCGH/man/runTilingArray.Rd snapCGH/man/sim.structure.Rd snapCGH/man/zero.length.distr.non.tiled.Rd snapCGH/man/zero.length.distr.tiled.Rd snapCGH/man/zoomChromosome.Rd snapCGH/man/zoomGenome.Rd
snapCGH/src
snapCGH/src/header.h
snapCGH/src/optimizer.c
snapCGH/vignettes
snapCGH/vignettes/snapCGHguide.Rnw
snapCGH/vignettes/zoomChromosome.jpg
snapCGH/vignettes/zoomGenome.jpg

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