Entry: aCGH
Aliases: aCGH create.aCGH log2.ratios clones.info is.aCGH dim.aCGH num.clones nrow.aCGH num.samples num.chromosomes ncol.aCGH clone.names row.names.aCGH rownames.aCGH clone.names<- row.names<-.aCGH rownames<-.aCGH col.names.aCGH col.names<-.aCGH colnames.aCGH colnames<-.aCGH sample.names sample.names<- log2.ratios.imputed log2.ratios.imputed<- hmm hmm<- hmm.merged hmm.merged<- sd.samples sd.samples<- genomic.events genomic.events<- phenotype phenotype<- [.aCGH print.aCGH summary.aCGH plot.aCGH minna maxna corna floor.func lengthNumFunc propNumFunc subset.hmm subset.hmm.merged ex.acgh.hmm
Keywords: classes
Description: Class aCGH
URL: ../../../library/aCGH/html/aCGH.html

Entry: aCGH.process
Aliases: aCGH.process
Keywords: file
Description: Process data in aCGH object
URL: ../../../library/aCGH/html/aCGH.process.html

Entry: aCGH.read.Sprocs
Aliases: aCGH.read.Sprocs dotify.names read.Sproc.files extract.clones.info maxdiff.func mincorr.func
Keywords: file
Description: Create object of class "aCGH" from Sproc files
URL: ../../../library/aCGH/html/aCGH.read.Sprocs.html

Entry: aCGH.test
Aliases: aCGH.test mt.maxT mt.minP
Keywords: htest
Description: Testing association of aCGH clones with censored or continuous outcomes
URL: ../../../library/aCGH/html/aCGH.test.html

Entry: clusterGenome
Aliases: clusterGenome plotvalChrom.func plotValGenome plotValChrom plotChrom
Keywords: hplot cluster
Description: clustering and heatmap
URL: ../../../library/aCGH/html/clusterGenome.html

Entry: colorectal
Aliases: colorectal clones.info.ex log2.ratios.ex pheno.type.ex
Keywords: datasets
Description: Colorectal array CGH dataset
URL: ../../../library/aCGH/html/colorectal.html

Entry: computeSD.func
Aliases: computeSD.func computeSD.Samples
Keywords: models
Description: Function to estimate experimental variability of a sample
URL: ../../../library/aCGH/html/computeSD.func.html

Entry: fga.func
Aliases: fga.func
Keywords: htest
Description: Function to compute fraction of genome altered for each sample
URL: ../../../library/aCGH/html/fga.func.html

Entry: find.genomic.events
Aliases: find.genomic.events
Keywords: models
Description: Finds the genomic events associated with each of the array CGH samples
URL: ../../../library/aCGH/html/find.genomic.events.html

Entry: find.hmm.states
Aliases: find.hmm.states hmm.run.func as.matrix.dist plotChrom.hmm.func plotCGH.hmm.func smoothData.func thresholdData.func plotChrom.samples.func plotChrom.grey.samples.func
Keywords: models
Description: Determines states of the clones
URL: ../../../library/aCGH/html/find.hmm.states.html

Entry: findAber.func
Aliases: findAber.func
Keywords: models
Description: Function to determines focal aberrations
URL: ../../../library/aCGH/html/findAber.func.html

Entry: findAmplif.func
Aliases: findAmplif.func
Keywords: models
Description: Function to determine high level amplifications
URL: ../../../library/aCGH/html/findAmplif.func.html

Entry: findOutliers.func
Aliases: findOutliers.func
Keywords: models
Description: Function to identify outlier clones
URL: ../../../library/aCGH/html/findOutliers.func.html

Entry: findTrans.func
Aliases: findTrans.func
Keywords: models
Description: Funtion identifying the transitions
URL: ../../../library/aCGH/html/findTrans.func.html

Entry: gainLoss
Aliases: gainLoss
Keywords: htest
Description: Function to compute proportion of gains and losses for each clones
URL: ../../../library/aCGH/html/gainLoss.html

Entry: heatmap
Aliases: heatmap
Keywords: hplot cluster
Description: Creates heatmap array CGH objects
URL: ../../../library/aCGH/html/heatmap.html

Entry: human.chrom.info.Jul03
Aliases: human.chrom.info.Jul03
Keywords: datasets
Description: Basic Chromosomal Information for UCSC Human Genome Assembly July 2003 freeze
URL: ../../../library/aCGH/html/human.chrom.info.Jul03.html

Entry: human.chrom.info.May04
Aliases: human.chrom.info.May04
Keywords: datasets
Description: Basic Chromosomal Information for UCSC Human Genome Assembly May 2004 freeze
URL: ../../../library/aCGH/html/human.chrom.info.May04.html

Entry: impute.HMM
Aliases: impute.HMM
Keywords: models
Description: Imputing log2 ratios using HMM
URL: ../../../library/aCGH/html/impute.HMM.html

Entry: impute.lowess
Aliases: impute.lowess
Keywords: models
Description: Imputing log2 ratios
URL: ../../../library/aCGH/html/impute.lowess.html

Entry: mergeFunc
Aliases: mergeFunc mergeHmmStates
Keywords: models
Description: Funtion to merge states based on their state means
URL: ../../../library/aCGH/html/mergeFunc.html

Entry: mergeLevels
Aliases: mergeLevels combine.func
Keywords: htest
Description: mergeLevels
URL: ../../../library/aCGH/html/mergeLevels.html

Entry: plotFreqStat
Aliases: plotFreqStat changeProp.func changeProp.overall.func table.bac.func lengthGain.na propGain.na lengthLoss.na propLoss.na prop.na create.resT plotFreqStatColors plotFreqStatGrey plotFreqGivenStat plotfreqGivenStatFinalColors plotfreq.stat.final.func plotfreq.stat.chrom.final.func plotfreq.givenstat.final.colors.func
Keywords: htest hplot
Description: frequency plots and significance analysis
URL: ../../../library/aCGH/html/plotFreqStat.html

Entry: plotGenome
Aliases: plotGenome plotGene plotGeneSign maPalette plotCGH.func
Keywords: hplot
Description: Plots the genome
URL: ../../../library/aCGH/html/plotGenome.html

Entry: plotHmmStates
Aliases: plotHmmStates plotHmmStatesNew
Keywords: hplot
Description: Plotting the estimated hmm states and log2 ratios for each sample.
URL: ../../../library/aCGH/html/plotHmmStates.html

Entry: plotSummaryProfile
Aliases: plotSummaryProfile
Keywords: hplot
Description: plotSummaryProfile
URL: ../../../library/aCGH/html/plotSummaryProfile.html

Entry: states.hmm.func
Aliases: states.hmm.func
Keywords: models
Description: A function to fit unsupervised Hidden Markov model
URL: ../../../library/aCGH/html/states.hmm.func.html

Entry: summarize.clones
Aliases: summarize.clones
Keywords: models
Description: Extracting summary information for all clones
URL: ../../../library/aCGH/html/summarize.clones.html

Entry: threshold.func
Aliases: threshold.func
Keywords: htest
Description: Function to indicate gain or loss for each clone for each sample
URL: ../../../library/aCGH/html/threshold.func.html
