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A C D E F G H I L M N P R S T misc
| Function to estimate experimental variability of a sample |
| aCGH | Class aCGH |
| aCGH.read.Sprocs | Create object of class "aCGH" from Sproc files |
| aCGH.test | frequency plots and significance analysis |
| as.matrix.dist | Determines states of the clones |
| changeProp.func | frequency plots and significance analysis |
| changeProp.overall.func | frequency plots and significance analysis |
| clone.names | Class aCGH |
| clones.info | Class aCGH |
| clones.info.ex | Colorectal array CGH dataset |
| col.names.aCGH | Class aCGH |
| colnames.aCGH | Class aCGH |
| colorectal | Colorectal array CGH dataset |
| computeSD.func | Function to estimate experimental variability of a sample |
| computeSD.Samples | Function to estimate experimental variability of a sample |
| corna | Class aCGH |
| create.aCGH | Class aCGH |
| dim.aCGH | Class aCGH |
| dotify.names | Create object of class "aCGH" from Sproc files |
| extract.clones.info | Create object of class "aCGH" from Sproc files |
| find.genomic.events | Finds the genomic events associated with each of the array CGH samples |
| find.hmm.states | Determines states of the clones |
| findAber.func | Function to determines focal aberrations |
| findAmplif.func | Function to determine high level amplifications |
| findOutliers.func | Function to identify outlier clones |
| findTrans.func | Funtion identifying the transitions |
| floor.func | Class aCGH |
| gainloss.func | frequency plots and significance analysis |
| genomic.events | Class aCGH |
| heatmap | Default method for plotting array CGH objects |
| hmm | Class aCGH |
| hmm.run.func | Determines states of the clones |
| human.chrom.info.Jul03 | Basic Chromosomal Information for UCSC Human Genome Assembly July 2003 freeze |
| impute.lowess | Imputing log2 ratios |
| is.aCGH | Class aCGH |
| length.num.func | Class aCGH |
| lengthGain.na | frequency plots and significance analysis |
| lengthLoss.na | frequency plots and significance analysis |
| log2.ratios | Class aCGH |
| log2.ratios.ex | Colorectal array CGH dataset |
| log2.ratios.imputed | Class aCGH |
| maPalette | Plots the genome |
| maxna | Class aCGH |
| mergeFunc | Funtion to merge states based on their state means |
| minna | Class aCGH |
| mu1.func | Determines states of the clones |
| ncol.aCGH | Class aCGH |
| nrow.aCGH | Class aCGH |
| num.chromosomes | Class aCGH |
| num.clones | Class aCGH |
| num.samples | Class aCGH |
| pheno.type.ex | Colorectal array CGH dataset |
| phenotype | Class aCGH |
| plot.aCGH | Class aCGH |
| plotCGH.func | Plots the genome |
| plotCGH.hmm.func | Determines states of the clones |
| plotChrom | clustering and heatmap |
| plotChrom.grey.samples.func | Determines states of the clones |
| plotChrom.hmm.func | Determines states of the clones |
| plotChrom.samples.func | Determines states of the clones |
| plotfreq.givenstat.final.colors.func | frequency plots and significance analysis |
| plotfreq.stat.chrom.final.func | frequency plots and significance analysis |
| plotfreq.stat.final.func | frequency plots and significance analysis |
| plotFreqGivenStat | frequency plots and significance analysis |
| plotfreqGivenStatFinalColors | frequency plots and significance analysis |
| plotFreqStat | frequency plots and significance analysis |
| plotFreqStatColors | frequency plots and significance analysis |
| plotFreqStatGrey | frequency plots and significance analysis |
| plotGene | Plots the genome |
| plotGeneSign | Plots the genome |
| plotGenome | Plots the genome |
| plotHmmStates | Plotting the estimated hmm states and log2 ratios for each sample. |
| plotHmmStatesNew | Plotting the estimated hmm states and log2 ratios for each sample. |
| plotSummaryProfile | plotSummaryProfile |
| plotValChrom | clustering and heatmap |
| plotvalChrom.func | clustering and heatmap |
| plotValGenome | clustering and heatmap |
| plotvalGenome.func | clustering and heatmap |
| print.aCGH | Class aCGH |
| prop.na | frequency plots and significance analysis |
| prop.num.func | Class aCGH |
| propGain.na | frequency plots and significance analysis |
| propLoss.na | frequency plots and significance analysis |
| read.Sproc.files | Create object of class "aCGH" from Sproc files |
| row.names.aCGH | Class aCGH |
| rownames.aCGH | Class aCGH |
| sample.names | Class aCGH |
| sd.samples | Class aCGH |
| smoothData.func | Determines states of the clones |
| states.hmm.func | A function to fit unsupervised Hidden Markov model |
| subset.hmm | Class aCGH |
| summary.aCGH | Class aCGH |
| table.bac.func | frequency plots and significance analysis |
| threshold.func | frequency plots and significance analysis |
| thresholdData.func | Determines states of the clones |
| [.aCGH | Class aCGH |