Man pages for Ringo
R Investigation of ChIP-chip Oligoarrays
| arrayImage | Function to visualize spatial distribution of raw intensities |
| asExprSet | converts a Ringo MAList into an ExpressionSet |
| autocorr | Function to compute auto-correlation of probe intensities |
| cherByThreshold | Function to identify chers based on thresholds |
| cherClass | Class "cher" - ChIP-enriched region |
| chipAlongChrom | Visualize ChIP intensities along the chromosome |
| chipAlongChromOld | Visualize ChIP intensities along the chromosome |
| compute_gc | Compute the GC content of DNA and probe sequences |
| computeRunningMedians | Function to compute running medians on a tiling expression... |
| compute_sliding_t | Function to compute sliding T statistics on a tiling... |
| corrPlot | Function to plot correlation of different samples |
| 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 |
| getFeats | Utility function to extract all features from a cherList |
| newCER | Create a list object of class cher |
| nimblegenNorm | Function to compute scaled log-ratios |
| nonzero | Methods for Function nonzero |
| plotAutocorr | Plots auto-correlation of probe intensities |
| plotBM | Visualization of a binary matrix |
| plot_cher | Plot identified Chers |
| posToProbeAnnoEnvironment | Function for creating a probeAnno environment |
| preprocess | Preprocess Raw ChIP-chip Intensities |
| probeAnnoClass | Class "probeAnno" |
| qopS4 | Class "qop" Quantiles Over Positions |
| quantilesOverPositions | show ChIP-chip data aligned over genome features, e.g. TSSs |
| readNimblegen | Function to read in Nimblegen Intensity Text Files |
| regionoverlap | Function to compute overlap of genomic regions |
| relateCERs | Relate found Chers to genomic features |
| Ringo-internal | Internal Ringo functions |
| sigGOTable | Obtain significant GO terms for a list of genes |
| sliding_meansd | Compute mean and standard deviation of scores in a sliding... |
| sliding_quantile | Compute quantile of scores in a sliding window |
| twoGaussiansNull | Estimate a threshold from Gaussian mixture distribution |
| upperBoundNull | function to estimate upper limit of null distribution |
| validProbeAnno | Function to check a probeAnno environment |
