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...

Functions

aCGH Man page
[.aCGH Man page
aCGH.process Man page
aCGH.read.Sprocs Man page
aCGH.test Man page
as.eSet Man page
as.matrix.dist Man page
changeProp.func Man page
changeProp.overall.func Man page
clone.names Man page
clone.names<- Man page
clones.info Man page
clones.info.ex Man page
clusterGenome Man page
col.names<-.aCGH Man page
col.names.aCGH Man page
colnames<-.aCGH Man page
colnames.aCGH Man page
colorectal Man page
combine.func Man page
computeSD.func Man page
computeSD.Samples Man page
corna Man page
create.aCGH Man page
create.resT Man page
dim.aCGH Man page
dotify.names Man page
ex.acgh.hmm Man page
ex.acgh.hmm Man page
ex.acgh.hmm Man page
extract.clones.info Man page
fga.func Man page
findAber.func Man page
findAmplif.func Man page
find.genomic.events Man page
find.hmm.states Man page
findOutliers.func Man page
findTrans.func Man page
floorFunc Man page
gainLoss Man page
genomic.events Man page
genomic.events<- Man page
heatmap Man page
hmm Man page
hmm<- Man page
hmm.merged Man page
hmm.merged<- Man page
hmm.run.func Man page
human.chrom.info.Jul03 Man page
human.chrom.info.May04 Man page
impute.HMM Man page
impute.HMM Man page
impute.lowess Man page
is.aCGH Man page
is.even Man page
is.odd Man page
lengthGain.na Man page
lengthLoss.na Man page
lengthNumFunc Man page
log2.ratios Man page
log2.ratios.ex Man page
log2.ratios.imputed Man page
log2.ratios.imputed<- Man page
maPalette Man page
maxdiff.func Man page
maxna Man page
mergeFunc Man page
mergeHmmStates Man page
mergeLevels Man page
mincorr.func Man page
minna Man page
mt.maxT Man page
mt.minP Man page
ncol.aCGH Man page
nrow.aCGH Man page
num.chromosomes Man page
num.clones Man page
num.samples Man page
phenotype Man page
phenotype<- Man page
pheno.type.ex Man page
plot.aCGH Man page
plotCGH.func Man page
plotCGH.hmm.func Man page
plotChrom Man page
plotChrom.grey.samples.func Man page
plotChrom.hmm.func Man page
plotChrom.samples.func Man page
plotFreqGivenStat Man page
plotfreqGivenStatFinalColors Man page
plotfreq.givenstat.final.colors.func Man page
plotFreqStat Man page
plotfreq.stat.chrom.final.func Man page
plotFreqStatColors Man page
plotfreq.stat.final.func Man page
plotFreqStatGrey Man page
plotGene Man page
plotGeneSign Man page
plotGenome Man page
plotHmmStates Man page
plotHmmStatesNew Man page
plotSummaryProfile Man page
plotValChrom Man page
plotvalChrom.func Man page
plotValGenome Man page
print.aCGH Man page
propGain.na Man page
propLoss.na Man page
prop.na Man page
propNumFunc Man page
read.Sproc.files Man page
row.names<-.aCGH Man page
row.names.aCGH Man page
rownames<-.aCGH Man page
rownames.aCGH Man page
sample.names Man page
sample.names<- Man page
sd.samples Man page
sd.samples<- Man page
smoothData.func Man page
states.hmm.func Man page
subset.hmm Man page
subset.hmm.merged Man page
summarize.clones Man page
summary.aCGH Man page
table.bac.func Man page
thresholdData.func Man page
threshold.func Man page
threshold.func Man page

Files

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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