quantsmooth: Quantile smoothing and genomic visualization of array data

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.

Author
Jan Oosting, Paul Eilers, Renee Menezes
Date of publication
None
Maintainer
Jan Oosting <j.oosting@lumc.nl>
License
GPL-2
Version
1.40.0

View on Bioconductor

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
scaleto
Scales data within a range to a new range

Files in this package

quantsmooth/DESCRIPTION
quantsmooth/NAMESPACE
quantsmooth/R
quantsmooth/R/quantsmooth.R
quantsmooth/R/quantsmoothplot.R
quantsmooth/build
quantsmooth/build/vignette.rds
quantsmooth/data
quantsmooth/data-raw
quantsmooth/data-raw/chrombandsUCSC.R
quantsmooth/data/chr14.rda
quantsmooth/data/chrom.bands.hg18.rda
quantsmooth/data/chrom.bands.hg19.rda
quantsmooth/data/chrom.bands.hg38.rda
quantsmooth/data/chrom.bands.mm10.rda
quantsmooth/data/chrom.bands.rda
quantsmooth/inst
quantsmooth/inst/doc
quantsmooth/inst/doc/quantsmooth.R
quantsmooth/inst/doc/quantsmooth.Rnw
quantsmooth/inst/doc/quantsmooth.pdf
quantsmooth/man
quantsmooth/man/Chromosome14.Rd
quantsmooth/man/chrom.bands.Rd
quantsmooth/man/drawSimpleChrom.Rd
quantsmooth/man/getChangedIdx.Rd
quantsmooth/man/getChangedRegions.Rd
quantsmooth/man/getLambdaMin.Rd
quantsmooth/man/grid.chromosome.Rd
quantsmooth/man/lengthChromosome.Rd
quantsmooth/man/numericCHR.Rd
quantsmooth/man/paintCytobands.Rd
quantsmooth/man/plotChromosome.Rd
quantsmooth/man/plotSmoothed.Rd
quantsmooth/man/position2Cytoband.Rd
quantsmooth/man/prepareGenomePlot.Rd
quantsmooth/man/quantsmooth.Rd
quantsmooth/man/quantsmooth.cv.Rd
quantsmooth/man/quantsmooth.seg.rd
quantsmooth/man/scaleto.Rd
quantsmooth/vignettes
quantsmooth/vignettes/quantsmooth.Rnw