arrayImage |
Function to visualize spatial distribution of raw intensities |
arrayName |
Class "probeAnno" |
arrayName,probeAnno-method |
Class "probeAnno" |
arrayName<- |
Class "probeAnno" |
arrayName<-,probeAnno,character-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,cher-method |
Class "cher" - ChIP-enriched region |
cellType<- |
Class "cher" - ChIP-enriched region |
cellType<-,cher,character-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,probeAnno-method |
Class "probeAnno" |
coerce,environment,probeAnno-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,probeAnno-method |
Class "probeAnno" |
genome<- |
Class "probeAnno" |
genome<-,probeAnno,character-method |
Class "probeAnno" |
get,character,missing,probeAnno,missing,missing-method |
Class "probeAnno" |
getFeats |
Utility function to extract all features from a cherList |
getFeatures |
Utility function to extract all features from a cherList |
image,RGList-method |
Function to visualize spatial distribution of raw intensities |
image.RGList |
Function to visualize spatial distribution of raw intensities |
initialize,cher-method |
Class "cher" - ChIP-enriched region |
initialize,probeAnno-method |
Class "probeAnno" |
ls,probeAnno,missing,missing,missing,missing-method |
Class "probeAnno" |
nonzero |
Methods for Function nonzero |
nonzero,dgCMatrix-method |
Methods for Function nonzero |
nonzero,matrix-method |
Methods for Function nonzero |
nonzero,matrix.csr-method |
Methods for Function nonzero |
nonzero-methods |
Methods for Function nonzero |
nullUpperBound |
function to estimate upper limit of null distribution |
plot,cher,ExpressionSet-method |
Plot identified Chers |
plot,cher,missing-method |
Plot identified Chers |
plot,ExpressionSet,probeAnno-method |
Visualize ChIP intensities along the chromosome |
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,cher-method |
Class "cher" - ChIP-enriched region |
probes,cherList-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,cher-method |
Class "cher" - ChIP-enriched region |
show,probeAnno-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,cher-method |
Class "cher" - ChIP-enriched region |
upperBoundNull |
function to estimate upper limit of null distribution |
[,probeAnno,ANY,ANY,ANY-method |
Class "probeAnno" |
[,probeAnno-method |
Class "probeAnno" |
[<-,probeAnno,ANY,ANY,ANY-method |
Class "probeAnno" |
[<-,probeAnno-method |
Class "probeAnno" |