quantsmooth (version 1.38.0)

Quantile smoothing and genomic visualization of array data

Description

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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Version

1.38.0

License

GPL-2

Maintainer

Jan Oosting

Last Published

February 15th, 2017

Functions in quantsmooth (1.38.0)

numericCHR

Conversion of chromosome IDs between numeric and character

lengthChromosome

Retrieve chromosomal length

paintCytobands

Paint a chromosomal idiogram

quantsmooth.cv

drawSimpleChrom

Draw chromosome-like icons

helperFunctions

arraysmooth Helper functions

chrom.bands

Dataset of human chromosomes and their banding patterns

position2Cytoband

Determine cytoband position based on location of probe

plotChromosome

Wrapper for plotSmoothed

prepareGenomePlot

Set up a full genome plot

Chromosome14

Example data from several quantitative genomic methods

plotSmoothed

scaleto

Scales data within a range to a new range

quantsmooth

grid.chromosome

Draw a chromosome using the grid package

getLambdaMin

quantsmooth.seg

getChangedRegions