SNPchip: Visualizations for copy number alterations

Functions for plotting SNP array data; maintained for historical reasons

Author
Robert Scharpf <rscharpf@jhu.edu> and Ingo Ruczinski
Date of publication
None
Maintainer
Robert Scharpf <rscharpf@jhu.edu>
License
LGPL (>= 2)
Version
2.20.0
URLs

View on Bioconductor

Man pages

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

Files in this package

SNPchip/DESCRIPTION
SNPchip/NAMESPACE
SNPchip/R
SNPchip/R/AllGenerics.R
SNPchip/R/annotation-functions.R
SNPchip/R/coerce-methods.R
SNPchip/R/grid-functions.R
SNPchip/R/idiogram-functions.R
SNPchip/R/panel-functions.R
SNPchip/R/xyplot-methods.R
SNPchip/R/zzz.R
SNPchip/build
SNPchip/build/vignette.rds
SNPchip/changelog
SNPchip/inst
SNPchip/inst/CITATION
SNPchip/inst/doc
SNPchip/inst/doc/PlottingIdiograms.R
SNPchip/inst/doc/PlottingIdiograms.Rnw
SNPchip/inst/doc/PlottingIdiograms.pdf
SNPchip/inst/extdata
SNPchip/inst/extdata/cytoBand_hg18.txt
SNPchip/inst/extdata/cytoBand_hg19.txt
SNPchip/inst/extdata/gap_hg18.rda
SNPchip/inst/extdata/gap_hg19.rda
SNPchip/inst/hg18
SNPchip/inst/unitTests
SNPchip/inst/unitTests/Makefile
SNPchip/inst/unitTests/test_xyplot.R
SNPchip/man
SNPchip/man/arrangeFigs.Rd
SNPchip/man/arrangeSideBySide.Rd
SNPchip/man/centromere.Rd
SNPchip/man/dataFrame-methods.Rd
SNPchip/man/dataFrame.Rd
SNPchip/man/defunct.Rd
SNPchip/man/getCytoband.rd
SNPchip/man/latticeFigs.Rd
SNPchip/man/plotIdiogram.Rd
SNPchip/man/xypanel.Rd
SNPchip/man/xypanelBaf.Rd
SNPchip/man/xyplot.Rd
SNPchip/man/xyplotLrrBaf.Rd
SNPchip/tests
SNPchip/tests/doRUnit.R
SNPchip/vignettes
SNPchip/vignettes/PlottingIdiograms.Rnw
SNPchip/vignettes/refs.bib