A C D E F G H I L M N P R S T misc
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 continuous outcomes |
as.matrix.dist | Determines states of the clones |
changeProp.func | frequency plots and significance analysis |
changeProp.overall.func | frequency plots and significance analysis |
clone.names | Class aCGH |
clone.names<- | Class aCGH |
clones.info | Class aCGH |
clones.info.ex | Colorectal array CGH dataset |
clusterGenome | clustering and heatmap |
col.names.aCGH | Class aCGH |
colnames.aCGH | Class aCGH |
colorectal | Colorectal array CGH dataset |
combine.func | mergeLevels |
computeSD.func | Function to estimate experimental variability of a sample |
computeSD.Samples | Function to estimate experimental variability of a sample |
corna | Class aCGH |
create.aCGH | Class aCGH |
create.resT | frequency plots and significance analysis |
dim.aCGH | Class aCGH |
dotify.names | Create object of class "aCGH" from Sproc files |
ex.acgh.hmm | Class aCGH |
extract.clones.info | Create object of class "aCGH" from Sproc files |
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 |
find.hmm.states | Determines states of the clones |
findAber.func | Function to determines focal aberrations |
findAmplif.func | Function to determine high level amplifications |
findOutliers.func | Function to identify outlier clones |
findTrans.func | Funtion identifying the transitions |
floorFunc | Class aCGH |
gainLoss | Function to compute proportion of gains and losses for each clones |
genomic.events | Class aCGH |
genomic.events<- | Class aCGH |
heatmap | Creates heatmap array CGH objects |
hmm | Class aCGH |
hmm.run.func | Determines states of the clones |
human.chrom.info.Jul03 | Basic Chromosomal Information for UCSC Human Genome Assembly July 2003 freeze |
human.chrom.info.May04 | Basic Chromosomal Information for UCSC Human Genome Assembly May 2004 freeze |
impute.HMM | Imputing log2 ratios using HMM |
impute.lowess | Imputing log2 ratios |
is.aCGH | Class aCGH |
lengthGain.na | frequency plots and significance analysis |
lengthLoss.na | frequency plots and significance analysis |
lengthNumFunc | Class aCGH |
log2.ratios | Class aCGH |
log2.ratios.ex | Colorectal array CGH dataset |
log2.ratios.imputed | Class aCGH |
log2.ratios.imputed<- | Class aCGH |
maPalette | Plots the genome |
maxdiff.func | Create object of class "aCGH" from Sproc files |
maxna | Class aCGH |
mergeFunc | Funtion to merge states based on their state means |
mergeHmmStates | Funtion to merge states based on their state means |
mergeLevels | mergeLevels |
mincorr.func | Create object of class "aCGH" from Sproc files |
minna | Class aCGH |
mt.maxT | Testing association of aCGH clones with censored or continuous outcomes |
mt.minP | Testing association of aCGH clones with censored or continuous outcomes |
ncol.aCGH | Class aCGH |
nrow.aCGH | Class aCGH |
num.chromosomes | Class aCGH |
num.clones | Class aCGH |
num.samples | Class aCGH |
pheno.type.ex | Colorectal array CGH dataset |
phenotype | Class aCGH |
plot.aCGH | Class aCGH |
plotCGH.func | Plots the genome |
plotCGH.hmm.func | Determines states of the clones |
plotChrom | clustering and heatmap |
plotChrom.grey.samples.func | Determines states of the clones |
plotChrom.hmm.func | Determines states of the clones |
plotChrom.samples.func | Determines states of the clones |
plotfreq.givenstat.final.colors.func | frequency plots and significance analysis |
plotfreq.stat.chrom.final.func | frequency plots and significance analysis |
plotfreq.stat.final.func | frequency plots and significance analysis |
plotFreqGivenStat | frequency plots and significance analysis |
plotfreqGivenStatFinalColors | frequency plots and significance analysis |
plotFreqStat | frequency plots and significance analysis |
plotFreqStatColors | frequency plots and significance analysis |
plotFreqStatGrey | frequency plots and significance analysis |
plotGene | Plots the genome |
plotGeneSign | Plots the genome |
plotGenome | Plots the genome |
plotHmmStates | Plotting the estimated hmm states and log2 ratios for each sample. |
plotHmmStatesNew | Plotting the estimated hmm states and log2 ratios for each sample. |
plotSummaryProfile | plotSummaryProfile |
plotValChrom | clustering and heatmap |
plotvalChrom.func | clustering and heatmap |
plotValGenome | clustering and heatmap |
print.aCGH | Class aCGH |
prop.na | frequency plots and significance analysis |
propGain.na | frequency plots and significance analysis |
propLoss.na | frequency plots and significance analysis |
propNumFunc | Class aCGH |
read.Sproc.files | Create object of class "aCGH" from Sproc files |
row.names.aCGH | Class aCGH |
rownames.aCGH | Class aCGH |
sample.names | Class aCGH |
sample.names<- | Class aCGH |
sd.samples | Class aCGH |
sd.samples<- | Class aCGH |
smoothData.func | Determines states of the clones |
states.hmm.func | A function to fit unsupervised Hidden Markov model |
subset.hmm | Class aCGH |
summarize.clones | Extracting summary information for all clones |
summary.aCGH | Class aCGH |
table.bac.func | frequency plots and significance analysis |
threshold.func | Function to indicate gain or loss for each clone for each sample |
thresholdData.func | Determines states of the clones |
[.aCGH | Class aCGH |