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Version
1.50.0
1.48.0
1.46.0
1.44.0
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Version
1.50.0
License
GPL-2
Maintainer
Peter Dimitrov
Last Published
April 15th, 2010
Functions in aCGH (1.50.0)
Search functions
aCGH.test
Testing association of aCGH clones with censored or continuous outcomes
clusterGenome
clustering and heatmap
impute.lowess
Imputing log2 ratios
mergeFunc
Funtion to merge states based on their state means
findAmplif.func
Function to determine high level amplifications
findOutliers.func
Function to identify outlier clones
plotSummaryProfile
plotSummaryProfile
states.hmm.func
A function to fit unsupervised Hidden Markov model
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
human.chrom.info.May04
Basic Chromosomal Information for UCSC Human Genome Assembly May 2004 freeze
impute.HMM
Imputing log2 ratios using HMM
aCGH.process
Process data in aCGH object
aCGH.read.Sprocs
Create object of class "aCGH" from Sproc files
mergeLevels
mergeLevels
plotFreqStat
frequency plots and significance analysis
colorectal
Colorectal array CGH dataset
computeSD.func
Function to estimate experimental variability of a sample
findTrans.func
Funtion identifying the transitions
gainLoss
Function to compute proportion of gains and losses for each clones
plotHmmStates
Plotting the estimated hmm states and log2 ratios for each sample.
plotGenome
Plots the genome
find.hmm.states
Determines states of the clones
findAber.func
Function to determines focal aberrations
heatmap
Creates heatmap array CGH objects
human.chrom.info.Jul03
Basic Chromosomal Information for UCSC Human Genome Assembly July 2003 freeze
summarize.clones
Extracting summary information for all clones
threshold.func
Function to indicate gain or loss for each clone for each sample