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Helper function for arranging multipanel displays of log R ratios and B allele frequencing in a single figure
● Data Source:
BioConductor
● Keywords: hplot
● Alias: arrangeFigs
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For visualizing copy number alterations, it is often helpful to plot estimates of copy number along with the corresponding estimate of the B allele frequencies. Creating a trellis object for the copy number estimates and a separate trellis object for the B allele frequencies, this function can be used to arrange the two trellis objects side by side on a grid.
● Data Source:
BioConductor
● Keywords: hplot
● Alias: arrangeSideBySide
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centromere
(Package: SNPchip) :
Coordinates of centromere
Extracts coordinates of centromere for a particular chromosome
● Data Source:
BioConductor
● Keywords: manip
● Alias: centromere
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dataFrame-methods
(Package: SNPchip) :
Construct a data.frame from genomic data for plotting
Construct a data.frame of genomic data (log R ratios and BAFs) from a RangedSummarizedExperiment with markers in the interval given by the GRanges object.
● Data Source:
BioConductor
● Keywords: methods
● Alias: dataFrame,GRanges,RangedSummarizedExperiment-method, dataFrame,GRanges,gSet-method, dataFrame-methods
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Generic function for coercing gSet objects to data.frame as a precursor to plotting with lattice
● Data Source:
BioConductor
● Keywords: manip, methods
● Alias: dataFrame
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The function, class, or data object you asked for has been deprecated.
● Data Source:
BioConductor
● Keywords: internal
● Alias: chromosomeAnnotation, cytoband, plotCytoband
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This function generates a data.frame with the respective cytoband names, chromosomes, Giemsa stain, and the start and end positions. These tables can then be used to plot chromosome idiograms. Currently, cytoband annotation for UCSC genome builds hg18 and hg19 are supported.
● Data Source:
BioConductor
● Keywords: misc
● Alias: getCytoband
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Generate trellis objects of log R ratios and B allele frequencies
● Data Source:
BioConductor
● Keywords: dplot
● Alias: latticeFigs
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plotIdiogram
(Package: SNPchip) :
Plots idiogram for one chromosome
Draw an idiogram for the specified chromosome.
● Data Source:
BioConductor
● Keywords: aplot
● Alias: plotCytoband2, plotIdiogram
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xypanel
(Package: SNPchip) :
A panel function for plotting copy number versus physical position
A panel function for xyplot for plotting copy number versus physical position.
● Data Source:
BioConductor
● Keywords: color, dplot
● Alias: xypanel
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