Man pages for snapCGH
Segmentation, normalisation and processing of aCGH data.

cbindCombine SegList Objects
chrominfo.MbBasic Chromosomal Information for UCSC Human Genome Assembly...
compareSegmentationsFunction for comparing segmentation methods to a known truth
convert.outputConverts the output from the simulation to a format which can...
dimRetrieve the Dimensions of an RGList, MAList or SegList...
dimnamesRetrieve the Dimension Names of an RGList, MAList or SegList...
filterFilter clones from sample
findBreakPointsReturns the start and end of segments.
find.param.fiveYields the output in a model with five underlying states
find.param.fourYields output when there are 4 underlying states
find.param.oneYields output when there is 1 underlying states
find.param.threeYields output when there are 3 underlying states
find.param.twoYields output when there are 2 underlying states
fit.modelFitting a heterogeneous HMM to the log2 ratios on a...
genomePlotPlots the genome
heatmapGenomeclustering and heatmap
IDProbesInteractive version of genomePlot
imputeMissingValuesImputing log2 ratios
LargeDataObjectLarge Data Object - class
log2ratiosExtracting log2 ratios
mergeStatesFunction to merge states based on their state means
non.zero.length.distr.non.tiledEmpirical distribution of segment lengths in non-tiled...
non.zero.length.distr.tiledEmpirical distribution of segment lengths in tiled regions...
plotSegmentedGenomePlots the genome
processCGHProcess data in an MAList
read.clonesinfoReading chromsome and positional information about each...
readPositionalInforeadPositionalInfo
removeByWeightsRemove clones based on a weights matrix
runBioHMMThis function implements the BioHMM
runDNAcopyResults of segmenting an MAList data object using the DNAcopy...
runGLADResults of segmenting an aCGHList data object using the GLAD...
runHMMA function to fit unsupervised Hidden Markov model
runTilingArrayResults of segmenting an MAList data object using the Picard...
SegListSegmentation States - class
sim.structureA function for simulating aCGH data and the corresponding...
Viterbi.fiveA scaled Viterbi algorithm for allocating clones to one of...
Viterbi.fourA scaled Viterbi algorithm for allocating clones to one of...
Viterbi.threeA scaled Viterbi algorithm for allocating clones to one of...
Viterbi.twoA scaled Viterbi algorithm for allocating clones to one of...
zero.length.distr.non.tiledEmpirical distribution of segment lengths in non-tiled...
zero.length.distr.tiledEmpirical distribution of segment lengths in tiled regions...
zoomChromosomeInteractive plot of a single chromsome
zoomGenomeInteractive plot of the whole genome
snapCGH documentation built on Nov. 17, 2017, 10:51 a.m.