SNPchip: Visualizations for copy number alterations
Version 2.22.0

Functions for plotting SNP array data; maintained for historical reasons

AuthorRobert Scharpf <rscharpf@jhu.edu> and Ingo Ruczinski
Bioconductor views CopyNumberVariation GeneticVariability SNP Visualization
Date of publicationNone
MaintainerRobert Scharpf <rscharpf@jhu.edu>
LicenseLGPL (>= 2)
Version2.22.0
URL http://www.biostat.jhsph.edu/~iruczins/software/snpchip.html
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("SNPchip")

Popular 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
defunct: SNPchip Deprecated
getCytoband: getCytoband
plotIdiogram: Plots idiogram for one chromosome
xyplotLrrBaf: xyplot lattice function for RangedData and oligoSnpSet...
See all...

All man pages Function index File listing

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
getCytoband: getCytoband
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...

Functions

arrangeFigs Man page Source code
arrangeSideBySide Man page Source code
centromere Man page Source code
centromereData Source code
chromosomeAnnotation Man page
chromosomeSize Source code
cleanname Source code
cytoband Man page
dataFrame Man page
dataFrame,GRanges,RangedSummarizedExperiment-method Man page
dataFrame,GRanges,gSet-method Man page
dataFrame-methods Man page
dataFrameFromRange Source code
dataFrameSummarizedExperiment Source code
drawCentromere Source code
drawCytobandWrapper Source code
drawXaxis Source code
drawYaxis Source code
getCytoband Man page Source code
latticeFigs Man page Source code
my.xypanel Source code
onAttach Source code
plotCytoband Man page Source code
plotCytoband2 Man page Source code
plotIdiogram Man page Source code
prepanel.fxn Source code
xypanel Man page Source code
xypanelBaf Man page Source code
xypanelRect Source code
xyplot Man page
xyplot,formula,BeadStudioSet-method Man page
xyplot,formula,gSet-method Man page
xyplot2 Man page Source code
xyplot2,formula,SnpSet-method Man page
xyplot2,formula,gSet-method Man page
xyplotLrrBaf Man page Source code
xyplotOligoSnpSet Source code
xyplotRangeInOligoSnpSet Source code

Files

DESCRIPTION
NAMESPACE
R
R/AllGenerics.R
R/annotation-functions.R
R/coerce-methods.R
R/grid-functions.R
R/idiogram-functions.R
R/panel-functions.R
R/xyplot-methods.R
R/zzz.R
build
build/vignette.rds
changelog
inst
inst/CITATION
inst/doc
inst/doc/PlottingIdiograms.R
inst/doc/PlottingIdiograms.Rnw
inst/doc/PlottingIdiograms.pdf
inst/extdata
inst/extdata/cytoBand_hg18.txt
inst/extdata/cytoBand_hg19.txt
inst/extdata/gap_hg18.rda
inst/extdata/gap_hg19.rda
inst/hg18
inst/unitTests
inst/unitTests/Makefile
inst/unitTests/test_xyplot.R
man
man/arrangeFigs.Rd
man/arrangeSideBySide.Rd
man/centromere.Rd
man/dataFrame-methods.Rd
man/dataFrame.Rd
man/defunct.Rd
man/getCytoband.rd
man/latticeFigs.Rd
man/plotIdiogram.Rd
man/xypanel.Rd
man/xypanelBaf.Rd
man/xyplot.Rd
man/xyplotLrrBaf.Rd
tests
tests/doRUnit.R
vignettes
vignettes/PlottingIdiograms.Rnw
vignettes/refs.bib
SNPchip documentation built on May 20, 2017, 10:18 p.m.

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