# Classes and functions for Array Comparative Genomic Hybridization data

## Documentation for package ‘aCGH’ version 1.70.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Code demos. Use demo() to run them.

## Help Pages

A C D E F G H I L M N P R S T misc

## -- A --

aCGH | Class aCGH
aCGH.process | Process data in aCGH object
aCGH.read.Sprocs | Create object of class "aCGH" from Sproc files
aCGH.test | Testing association of aCGH clones with censored or continuous outcomes
as.matrix.dist | Determines states of the clones

## -- C --

changeProp.func | frequency plots and significance analysis
changeProp.overall.func | frequency plots and significance analysis
clone.names | Class aCGH
clone.names<- | Class aCGH
clones.info | Class aCGH
clones.info.ex | Colorectal array CGH dataset
clusterGenome | clustering and heatmap
col.names.aCGH | Class aCGH
col.names<-.aCGH | Class aCGH
colnames.aCGH | Class aCGH
colnames<-.aCGH | Class aCGH
colorectal | Colorectal array CGH dataset
combine.func | mergeLevels
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
create.resT | frequency plots and significance analysis

## -- D --

dim.aCGH | Class aCGH
dotify.names | Create object of class "aCGH" from Sproc files

## -- E --

ex.acgh.hmm | Class aCGH
extract.clones.info | Create object of class "aCGH" from Sproc files

## -- F --

fga.func | Function to compute fraction of genome altered for each sample
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
floorFunc | Class aCGH

## -- G --

gainLoss | Function to compute proportion of gains and losses for each clones
genomic.events | Class aCGH
genomic.events<- | Class aCGH

## -- H --

heatmap | Creates heatmap array CGH objects
hmm | Class aCGH
hmm.merged | Class aCGH
hmm.merged<- | Class aCGH
hmm.run.func | Determines states of the clones
hmm<- | Class aCGH
human.chrom.info.Jul03 | Basic Chromosomal Information for UCSC Human Genome Assembly July 2003 freeze
human.chrom.info.May04 | Basic Chromosomal Information for UCSC Human Genome Assembly May 2004 freeze

## -- I --

impute.HMM | Imputing log2 ratios using HMM
impute.lowess | Imputing log2 ratios
is.aCGH | Class aCGH
is.even | Class aCGH
is.odd | Class aCGH

## -- L --

lengthGain.na | frequency plots and significance analysis
lengthLoss.na | frequency plots and significance analysis
lengthNumFunc | Class aCGH
log2.ratios | Class aCGH
log2.ratios.ex | Colorectal array CGH dataset
log2.ratios.imputed | Class aCGH
log2.ratios.imputed<- | Class aCGH

## -- M --

maPalette | Plots the genome
maxdiff.func | Create object of class "aCGH" from Sproc files
maxna | Class aCGH
mergeFunc | Funtion to merge states based on their state means
mergeHmmStates | Funtion to merge states based on their state means
mergeLevels | mergeLevels
mincorr.func | Create object of class "aCGH" from Sproc files
minna | Class aCGH
mt.maxT | Testing association of aCGH clones with censored or continuous outcomes
mt.minP | Testing association of aCGH clones with censored or continuous outcomes

## -- N --

ncol.aCGH | Class aCGH
nrow.aCGH | Class aCGH
num.chromosomes | Class aCGH
num.clones | Class aCGH
num.samples | Class aCGH

## -- P --

pheno.type.ex | Colorectal array CGH dataset
phenotype | Class aCGH
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
print.aCGH | Class aCGH
prop.na | frequency plots and significance analysis
propGain.na | frequency plots and significance analysis
propLoss.na | frequency plots and significance analysis
propNumFunc | Class aCGH

## -- R --

read.Sproc.files | Create object of class "aCGH" from Sproc files
row.names.aCGH | Class aCGH
row.names<-.aCGH | Class aCGH
rownames.aCGH | Class aCGH
rownames<-.aCGH | Class aCGH

## -- S --

sample.names | Class aCGH
sample.names<- | Class aCGH
sd.samples | 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
subset.hmm.merged | Class aCGH
summarize.clones | Extracting summary information for all clones
summary.aCGH | Class aCGH

## -- T --

table.bac.func | frequency plots and significance analysis
threshold.func | Function to indicate gain or loss for each clone for each sample
thresholdData.func | Determines states of the clones

## -- misc --

[.aCGH | Class aCGH