Classes and functions for Array Comparative Genomic Hybridization data

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Documentation for package ‘aCGH’ version 1.85.0

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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