quantsmooth: Quantile smoothing and genomic visualization of array data
Version 1.42.0

Implements quantile smoothing as introduced in: Quantile smoothing of array CGH data; Eilers PH, de Menezes RX; Bioinformatics. 2005 Apr 1;21(7):1146-53.

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AuthorJan Oosting, Paul Eilers, Renee Menezes
Bioconductor views CopyNumberVariation Visualization
Date of publicationNone
MaintainerJan Oosting <j.oosting@lumc.nl>
LicenseGPL-2
Version1.42.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("quantsmooth")

Man pages

chrom.bands: Dataset of human chromosomes and their banding patterns
Chromosome14: Example data from several quantitative genomic methods
drawSimpleChrom: Draw chromosome-like icons
getChangedIdx: arraysmooth Helper functions
getChangedRegions: getChangedRegions
getLambdaMin: getLambdaMin
grid.chromosome: Draw a chromosome using the grid package
lengthChromosome: Retrieve chromosomal length
numericCHR: Conversion of chromosome IDs between numeric and character
paintCytobands: Paint a chromosomal idiogram
plotChromosome: Wrapper for plotSmoothed
plotSmoothed: plotSmoothed
position2Cytoband: Determine cytoband position based on location of probe
prepareGenomePlot: Set up a full genome plot
quantsmooth: quantsmooth
quantsmooth.cv: quantsmooth.cv
quantsmooth.seg: quantsmooth.seg
scaleto: Scales data within a range to a new range

Functions

affy.cn Man page
affy.pos Man page
bac.cn Man page
bac.pos Man page
characterCHR Man page Source code
chr14 Man page
chrom.bands Man page
chrom.bands.hg18 Man page
chrom.bands.hg19 Man page
chrom.bands.hg38 Man page
chrom.bands.mm10 Man page
convertUCSCcytoband Source code
drawSimpleChrom Man page Source code
getChangedIdx Man page Source code
getChangedRegions Man page Source code
getChrombands Source code
getLambdaMin Man page Source code
grid.chromosome Man page Source code
ill.cn Man page
ill.pos Man page
lengthChromosome Man page Source code
numericCHR Man page Source code
paintCytobands Man page Source code
plotChromosome Man page Source code
plotSmoothed Man page Source code
position2Cytoband Man page Source code
prepareGenomePlot Man page Source code
qs.grid.semicircle Source code
qs.semicircle Source code
quantsmooth Man page Source code Source code
quantsmooth.cv Man page Source code
quantsmooth.seg Man page Source code
scaleto Man page Source code

Files

DESCRIPTION
NAMESPACE
R
R/quantsmooth.R
R/quantsmoothplot.R
build
build/vignette.rds
data
data-raw
data-raw/chrombandsUCSC.R
data/chr14.rda
data/chrom.bands.hg18.rda
data/chrom.bands.hg19.rda
data/chrom.bands.hg38.rda
data/chrom.bands.mm10.rda
data/chrom.bands.rda
inst
inst/doc
inst/doc/quantsmooth.R
inst/doc/quantsmooth.Rnw
inst/doc/quantsmooth.pdf
man
man/Chromosome14.Rd
man/chrom.bands.Rd
man/drawSimpleChrom.Rd
man/getChangedIdx.Rd
man/getChangedRegions.Rd
man/getLambdaMin.Rd
man/grid.chromosome.Rd
man/lengthChromosome.Rd
man/numericCHR.Rd
man/paintCytobands.Rd
man/plotChromosome.Rd
man/plotSmoothed.Rd
man/position2Cytoband.Rd
man/prepareGenomePlot.Rd
man/quantsmooth.Rd
man/quantsmooth.cv.Rd
man/quantsmooth.seg.rd
man/scaleto.Rd
vignettes
vignettes/quantsmooth.Rnw
quantsmooth documentation built on May 20, 2017, 9:15 p.m.