arrayImage | Function to visualize spatial distribution of raw intensities |
arrayName | Class "probeAnno" |
arrayName-method | Class "probeAnno" |
arrayName<- | Class "probeAnno" |
arrayName<--method | Class "probeAnno" |
asExpressionSet | converts a Ringo MAList into an ExpressionSet |
asExprSet | converts a Ringo MAList into an ExpressionSet |
autocor | Function to compute auto-correlation of probe intensities |
autocorr | Function to compute auto-correlation of probe intensities |
autocorrelation | Function to compute auto-correlation of probe intensities |
cellType | Class "cher" - ChIP-enriched region |
cellType-method | Class "cher" - ChIP-enriched region |
cellType<- | Class "cher" - ChIP-enriched region |
cellType<--method | Class "cher" - ChIP-enriched region |
Cher | Class "cher" - ChIP-enriched region |
cher | Class "cher" - ChIP-enriched region |
cher-class | Class "cher" - ChIP-enriched region |
cherByThreshold | Function to identify chers based on thresholds |
cherList | Class "cher" - ChIP-enriched region |
cherList-class | Class "cher" - ChIP-enriched region |
cherPlot | Plot identified Chers |
chipAlongChrom | Visualize ChIP intensities along the chromosome |
chromosomeNames | Class "probeAnno" |
chromosomeNames-method | Class "probeAnno" |
coerce-method | Class "probeAnno" |
compute.gc | Compute the GC content of DNA and probe sequences |
computeRunningMedians | Function to compute running medians on a tiling expression set |
computeSlidingT | Function to compute sliding T statistics on a tiling expression set |
corPlot | Function to plot correlation of different samples |
corrPlot | Function to plot correlation of different samples |
createProbeAnno | Function for creating a probeAnno environment |
exportCherList | Function to export cherList into a file |
extractProbeAnno | Build probeAnno from match positions in an RGList |
features2Probes | Function for mapping genomic features to probes |
findChersOnSmoothed | Find ChIP-enriched regions on smoothed ExpressionSet |
ftr2xys | Convert a NimbleScan ftr-file into a xys-file |
gccontent | Compute the GC content of DNA and probe sequences |
genome | Class "probeAnno" |
genome-method | Class "probeAnno" |
genome<- | Class "probeAnno" |
genome<--method | Class "probeAnno" |
get-method | Class "probeAnno" |
getFeats | Utility function to extract all features from a cherList |
getFeatures | Utility function to extract all features from a cherList |
image-method | Function to visualize spatial distribution of raw intensities |
image.RGList | Function to visualize spatial distribution of raw intensities |
initialize-method | Class "cher" - ChIP-enriched region |
initialize-method | Class "probeAnno" |
ls-method | Class "probeAnno" |
nonzero | Methods for Function nonzero |
nonzero-method | Methods for Function nonzero |
nonzero-methods | Methods for Function nonzero |
nullUpperBound | function to estimate upper limit of null distribution |
plot-method | Visualize ChIP intensities along the chromosome |
plot-method | Plot identified Chers |
plot.autocor.result | Plots auto-correlation of probe intensities |
plot.cher | Plot identified Chers |
plotAutocor | Plots auto-correlation of probe intensities |
plotBinaryMatrix | Visualization of a binary matrix |
plotBM | Visualization of a binary matrix |
plotCher | Plot identified Chers |
posToProbeAnno | Function for creating a probeAnno environment |
posToProbeAnnoEnvironment | Function for creating a probeAnno environment |
preprocess | Preprocess Raw ChIP-chip Intensities |
probeAnno | Class "probeAnno" |
probeAnno-class | Class "probeAnno" |
probeAnnoFromRGList | Build probeAnno from match positions in an RGList |
probes | Class "cher" - ChIP-enriched region |
probes-method | Class "cher" - ChIP-enriched region |
quantilesOverPositions | show ChIP-chip data aligned over genome features, e.g. TSSs |
readNimblegen | Function to read in Nimblegen Intensity Text Files |
region.overlap | Function to compute overlap of genomic regions |
regionOverlap | Function to compute overlap of genomic regions |
relateChers | Relate found Chers to genomic features |
show-method | Class "cher" - ChIP-enriched region |
show-method | Class "probeAnno" |
sliding.meansd | Compute mean and standard deviation of scores in a sliding window |
sliding.quantile | Compute quantile of scores in a sliding window |
slidingquantile | Compute quantile of scores in a sliding window |
twoGaussiansNull | Estimate a threshold from Gaussian mixture distribution |
update-method | Class "cher" - ChIP-enriched region |
upperBoundNull | function to estimate upper limit of null distribution |
[-method | Class "probeAnno" |
[<--method | Class "probeAnno" |