aCGH v1.50.0
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 |
| depends | base (>= 2.10) , cluster , multtest , R (>= 2.10) , survival |
| imports | Biobase , graphics , grDevices , methods , splines , stats , utils |
| Contributors | Peter Dimitrov, Jane Fridlyand |
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