writeGFF
(Package: Starr) :
write ChIP-chip data to a gff file
This function writes the all columns of the assayData to a gff file.
● Data Source:
BioConductor
● Keywords: IO
● Alias: writeGFF
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Writes a Nimblegen pos file from a given Affymetrix bpmap file.
● Data Source:
BioConductor
● Keywords: IO
● Alias: writePosFile
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writeWIG
(Package: Starr) :
write ChIP-chip data to a *.wig file
This function writes the all columns of the assayData to a wiggle file.
● Data Source:
BioConductor
● Keywords: IO
● Alias: writeWIG
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RGlist2ExpresionSet
(Package: Starr) :
Convert an RGlist to an ExpressionSet
This function converts an RGlist to an ExpressionSet.
● Data Source:
BioConductor
● Keywords: internal
● Alias: RGlist2ExpresionSet
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backgd.sd
(Package: Starr) :
Background parameters (internal function)
An internal function to be used by cmarrt.ma.
● Data Source:
BioConductor
● Keywords: internal
● Alias: backgd.sd
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This function allows the user to create a probeAnno environment that holds the mapping between probes on the array and their genomic match position(s). The function takes an Affymetrix bpmap file as input.
● Data Source:
BioConductor
● Keywords: manip
● Alias: bpmapToProbeAnno
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cmarrt.ma
(Package: Starr) :
Compute moving average statistics by incorporating the correlation structure
This function extends the moving average approach by incorporating the correlation structure. It also outputs the p-values of the standardized moving average statistics under the Gaussian approximation.
● Data Source:
BioConductor
● Keywords: manip
● Alias: cmarrt.ma
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cmarrt.peak
(Package: Starr) :
Obtain bound regions for a given error rate control
Obtain bound regions under a given error rate control using correction method from p.adjust.
● Data Source:
BioConductor
● Keywords: manip
● Alias: cmarrt.peak
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0 images
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correlate
(Package: Starr) :
Correlate the values of two named vectors
correlate calculates the correlation of a list of named vectors and a named vector. Only entries, existing in both vectors are used.
● Data Source:
BioConductor
● Keywords: internal
● Alias: correlate
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correlationPlot
(Package: Starr) :
correlation of ChIP signals to other data
correlationPlot The correlationPlot can be used to vizualize e.g. the correlation between the mean binding intensity of specific regions around annotated features and gene expression. The regions around the annotated features, that should be analyzed are defined in a data frame. Each row represents one region. In the upper panel of the plot, the correlation is plotted in a barplot. In the lower panel, the annotated feature and the regions defined in the data frame are shown.
● Data Source:
BioConductor
● Keywords: hplot
● Alias: correlationPlot
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