aCGH: Classes and functions for Array Comparative Genomic Hybridization data.

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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.

Author
Jane Fridlyand <jfridlyand@cc.ucsf.edu>, Peter Dimitrov <dimitrov@stat.Berkeley.EDU>
Date of publication
None
Maintainer
Peter Dimitrov <dimitrov@stat.Berkeley.EDU>
License
GPL-2
Version
1.52.0

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