aCGH v1.50.0

by Peter Dimitrov

Classes and functions for Array Comparative Genomic Hybridization data.

Functions for reading aCGH data from image analysis output files and clone information files, creation of aCGH S3 objects for storing these data. Basic methods for accessing/replacing, subsetting, printing and plotting aCGH objects.

Functions in aCGH

Name Description
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
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Details

Date 2010-04-15
License GPL-2
Collate aCGH.R aCGH.plotting.R aCGH.read.R aCGH.test.R clusterGenome.R funcs.dataplot.R heatmap.R hmm.R human.chrom.info.Jul03.R human.chrom.info.May04.R mergeLevels.R
LazyLoad yes
biocViews CopyNumberVariation, DataImport, Genetics

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