Man pages for Starr
Simple tiling array analysis of Affymetrix ChIP-chip data
| backgd.sd | Background parameters (internal function) |
| bpmapToProbeAnno | Creating a probeAnno object |
| cmarrt.ma | Compute moving average statistics by incorporating the... |
| cmarrt.peak | Obtain bound regions for a given error rate control |
| correlate | Correlate the values of two named vectors |
| correlationPlot | correlation of ChIP signals to other data |
| declare.bound | Declare bound probes for a given error rate control |
| densityscatter | Compute density of a scatterplot |
| expressionByFeature | Getting expression value by feature from an ExpressionSet |
| fill | Fill large spaces in one profile with NA |
| fillNA | Fill large spaces in profiles with NA |
| filterGenes | Filter Features/Genes |
| getFeatures | Getting profiles of one annotated features with a given... |
| getIntensites | Get profile of anntated features from a probe mapping |
| getMeans | Get mean ChIP-signal over annotated features |
| getProfiles | Get profiles of ChIP-signal over annotated features |
| getProfilesByBase | Get profiles of ChIP-signal over annotated features... |
| getRatio | Building ratio over experiments |
| heatmapplot | heatmapplot |
| intersection | Get the intersection of two named vectors |
| kde2dplot | Compute density of a scatterplot |
| list2matrix | Convert profile list to matrix |
| makeProbeAnno | Creating a probeAnno object |
| makeSplines | Fit splines to profiles |
| mapFeatures | Map middle positions of probes to annotated features |
| ma.stat | Compute moving average statistics and p-values |
| match_ac | Exact String matching using the Aho-Corasick algorithm |
| normalize.Probes | Normalization of probes |
| plot.boxes | boxplots of experiments |
| plot.cmarrt | Histogram of p-values and normal QQ plots for standardized MA... |
| plot.Density | density plots of experiments |
| plot.gcBias | Visualize GC-Bias of Hybridization |
| plot.image | Reconstruct the array image |
| plot.ma | M versus A plot |
| plot.posBias | Bias of hybridzation, depending on base position in sequence. |
| plotProfiles | Plotting ChIP profiles of one or more clusters |
| plot.ratioScatter | Plot ratios of all possible combinations of IP and CONTROL |
| plot.scatter | High level scatterplot of experiments |
| profileplot | Vizualize clusters |
| rankPercentile.normalize | Rank precentile Normalization |
| readCelFile | Read raw intensities from CEL files |
| read.gffAnno | Reading gff annotation |
| remap | Remap reporter sequences to the genome and create a new bpmap... |
| RGlist2ExpressionSet | Convert an RGlist to an ExpressionSet |
| rm.small.peak | Remove bound regions which consist of too few probes |
| sameLength | Make equal length of upstream and downstream regions in a... |
| singleclusterplot | single cluster plot |
| sort.by.genomic | Pre-process the data by genomic location |
| substract | Substract mean or median from data |
| whichIn | Map positions to intervals |
| windowxy | Get mfcol or mfrow for a number of plots to one device |
| writeGFF | write ChIP-chip data to a gff file |
| writePosFile | Creating a pos file |
| writeWIG | write ChIP-chip data to a *.wig file |
