Visualizations for copy number alterations


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Documentation for package ‘SNPchip’ version 2.16.0

Help Pages

arrangeFigs Arranging two trellis objects on a grid.
arrangeSideBySide Helper function to arrange two trellis objects side by side on a grid.
centromere Coordinates of centromere
dataFrame Generic function for coercing gSet objects to data.frame
dataFrame-method Construct a data.frame from genomic data for plotting
dataFrame-methods Construct a data.frame from genomic data for plotting
getCytoband getCytoband
latticeFigs Generate trellis objects of log R ratios and B allele frequencies
plotCytoband2 Plots idiogram for one chromosome
plotIdiogram Plots idiogram for one chromosome
xypanel A panel function for plotting copy number versus physical position
xypanelBaf Panel function for plotting copy number and B allele frequencies for a genomic interval.
xyplot2 Plot copy number and physical position for a set of genomic intervals.
xyplot2-method Plot copy number and physical position for a set of genomic intervals.
xyplotLrrBaf xyplot lattice function for RangedData and oligoSnpSet objects