Man pages for Bioconductor-mirror/Starr
Simple tiling array analysis of Affymetrix ChIP-chip data

backgd.sdBackground parameters (internal function)
bpmapToProbeAnnoCreating a probeAnno object
cmarrt.maCompute moving average statistics by incorporating the...
cmarrt.peakObtain bound regions for a given error rate control
correlateCorrelate the values of two named vectors
correlationPlotcorrelation of ChIP signals to other data
declare.boundDeclare bound probes for a given error rate control
densityscatterCompute density of a scatterplot
expressionByFeatureGetting expression value by feature from an ExpressionSet
fillFill large spaces in one profile with NA
fillNAFill large spaces in profiles with NA
filterGenesFilter Features/Genes
getFeaturesGetting profiles of one annotated features with a given...
getIntensitesGet profile of anntated features from a probe mapping
getMeansGet mean ChIP-signal over annotated features
getProfilesGet profiles of ChIP-signal over annotated features
getProfilesByBaseGet profiles of ChIP-signal over annotated features...
getRatioBuilding ratio over experiments
heatmapplotheatmapplot
intersectionGet the intersection of two named vectors
kde2dplotCompute density of a scatterplot
list2matrixConvert profile list to matrix
makeProbeAnnoCreating a probeAnno object
makeSplinesFit splines to profiles
mapFeaturesMap middle positions of probes to annotated features
ma.statCompute moving average statistics and p-values
match_acExact String matching using the Aho-Corasick algorithm
normalize.ProbesNormalization of probes
plot.boxesboxplots of experiments
plot.cmarrtHistogram of p-values and normal QQ plots for standardized MA...
plot.Densitydensity plots of experiments
plot.gcBiasVisualize GC-Bias of Hybridization
plot.imageReconstruct the array image
plot.maM versus A plot
plot.posBiasBias of hybridzation, depending on base position in sequence.
plotProfilesPlotting ChIP profiles of one or more clusters
plot.ratioScatterPlot ratios of all possible combinations of IP and CONTROL
plot.scatterHigh level scatterplot of experiments
profileplotVizualize clusters
rankPercentile.normalizeRank precentile Normalization
readCelFileRead raw intensities from CEL files
read.gffAnnoReading gff annotation
remapRemap reporter sequences to the genome and create a new bpmap...
RGlist2ExpressionSetConvert an RGlist to an ExpressionSet
rm.small.peakRemove bound regions which consist of too few probes
sameLengthMake equal length of upstream and downstream regions in a...
singleclusterplotsingle cluster plot
sort.by.genomicPre-process the data by genomic location
substractSubstract mean or median from data
whichInMap positions to intervals
windowxyGet mfcol or mfrow for a number of plots to one device
writeGFFwrite ChIP-chip data to a gff file
writePosFileCreating a pos file
writeWIGwrite ChIP-chip data to a *.wig file
Bioconductor-mirror/Starr documentation built on June 1, 2017, 2:27 a.m.