aCGH: 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.

AuthorJane Fridlyand <jfridlyand@cc.ucsf.edu>, Peter Dimitrov <dimitrov@stat.Berkeley.EDU>
Date of publicationNone
MaintainerPeter Dimitrov <dimitrov@stat.Berkeley.EDU>
LicenseGPL-2
Version1.52.0

View on Bioconductor

Man pages

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...

clusterGenome: clustering and heatmap

colorectal: Colorectal array CGH dataset

computeSD.func: Function to estimate experimental variability of a sample

fga.func: Function to compute fraction of genome altered for each...

findAber.func: Function to determines focal aberrations

findAmplif.func: Function to determine high level amplifications

find.genomic.events: Finds the genomic events associated with each of the array...

find.hmm.states: Determines states of the clones

findOutliers.func: Function to identify outlier clones

findTrans.func: Funtion identifying the transitions

gainLoss: Function to compute proportion of gains and losses for each...

heatmap: Creates heatmap array CGH objects

human.chrom.info.Jul03: Basic Chromosomal Information for UCSC Human Genome Assembly...

human.chrom.info.May04: Basic Chromosomal Information for UCSC Human Genome Assembly...

impute.HMM: Imputing log2 ratios using HMM

impute.lowess: Imputing log2 ratios

mergeFunc: Funtion to merge states based on their state means

mergeLevels: mergeLevels

plotFreqStat: frequency plots and significance analysis

plotGenome: Plots the genome

plotHmmStates: Plotting the estimated hmm states and log2 ratios for each...

plotSummaryProfile: plotSummaryProfile

states.hmm.func: A function to fit unsupervised Hidden Markov model

summarize.clones: Extracting summary information for all clones

threshold.func: Function to indicate gain or loss for each clone for each...

Files in this package

aCGH/DESCRIPTION
aCGH/NAMESPACE
aCGH/R
aCGH/R/aCGH.R aCGH/R/aCGH.plotting.R aCGH/R/aCGH.read.R aCGH/R/aCGH.test.R aCGH/R/clusterGenome.R aCGH/R/funcs.dataplot.R aCGH/R/heatmap.R aCGH/R/hmm.R aCGH/R/human.chrom.info.Jul03.R aCGH/R/human.chrom.info.May04.R aCGH/R/mergeLevels.R
aCGH/build
aCGH/build/vignette.rds
aCGH/data
aCGH/data/colorectal.rda
aCGH/data/datalist
aCGH/demo
aCGH/demo/00Index
aCGH/demo/aCGH.R
aCGH/inst
aCGH/inst/doc
aCGH/inst/doc/aCGH.R
aCGH/inst/doc/aCGH.Rnw
aCGH/inst/doc/aCGH.pdf
aCGH/inst/examples
aCGH/inst/examples/clones.info.ex.txt
aCGH/inst/examples/human.clones.info.Jul03.txt
aCGH/inst/examples/log2.ratios.ex.txt
aCGH/inst/examples/pheno.type.ex.txt
aCGH/inst/examples/sprocCR40.txt
aCGH/inst/examples/sprocCR43.txt
aCGH/man
aCGH/man/aCGH.Rd aCGH/man/aCGH.process.Rd aCGH/man/aCGH.read.Sprocs.Rd aCGH/man/aCGH.test.Rd aCGH/man/clusterGenome.Rd aCGH/man/colorectal.Rd aCGH/man/computeSD.func.Rd aCGH/man/fga.func.Rd aCGH/man/find.genomic.events.Rd aCGH/man/find.hmm.states.Rd aCGH/man/findAber.func.Rd aCGH/man/findAmplif.func.Rd aCGH/man/findOutliers.func.Rd aCGH/man/findTrans.func.Rd aCGH/man/gainLoss.Rd aCGH/man/heatmap.Rd aCGH/man/human.chrom.info.Jul03.Rd aCGH/man/human.chrom.info.May04.Rd aCGH/man/impute.HMM.Rd aCGH/man/impute.lowess.Rd aCGH/man/mergeFunc.Rd aCGH/man/mergeLevels.Rd aCGH/man/plotFreqStat.Rd aCGH/man/plotGenome.Rd aCGH/man/plotHmmStates.Rd aCGH/man/plotSummaryProfile.Rd aCGH/man/states.hmm.func.Rd aCGH/man/summarize.clones.Rd aCGH/man/threshold.func.Rd
aCGH/src
aCGH/src/Makevars
aCGH/src/hmm.cpp
aCGH/vignettes
aCGH/vignettes/aCGH.Rnw
aCGH/vignettes/aCGH.bib

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