Reconstruct tile image

Description

Generate an image of the local intensity average

Usage

## S4 method for signature 'SolexaIntensity'
TileImage(int,cycle,tile,channel=c('A','C','G','T'),ncell=30)
TileImage(int,...)

Arguments

Details

TileImage creates an image of the intensity on a tile, in a given channel and at a given cycle. The tile is divided into ncell*ncell cells and the average intensity in each cell is represented on a color scale.

Author(s)

Jacques Rougemont, Arnaud Amzallag, Christian Iseli, Laurent Farinelli, Ioannis Xenarios, Felix Naef

References

Probabilistic base calling of Solexa sequencing data, BMC Bioinformatics 2008, 9:431

Examples

path = SolexaPath(system.file("extdata", package="ShortRead"))
rolenv = SetModel(idsep="_")
int = readIntensities(path,pattern="s_1_0001",withVariability=FALSE)
par(mfrow=c(2,2))
for (c in c('A','C','G','T'))
    TileImage(int=int,cycle=1,tile=readInfo(int)$tile[1],channel=c,ncell=5)
int2 = TileNormalize(rolenv,int=int,cycles=1)
x11()
par(mfrow=c(2,2))
for (c in c('A','C','G','T'))
    TileImage(int=int2,cycle=1,tile=readInfo(int)$tile[1],channel=c,ncell=5)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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> library(Rolexa)
Error in library(Rolexa) : there is no package called 'Rolexa'
Execution halted