Plots3: Reconstruct tile image

In Rolexa: Statistical analysis of Solexa sequencing data

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

int	a SolexaIntensity object
cycle	the cycle to make an image of
tile	the tile to make an image of
channel	the channel ('A', 'C', 'G' or 'T') to make an image of
ncell	the number of divisions in each dimension for the image
...	additional arguments, ignored

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)

Rolexa documentation built on Oct. 5, 2016, 4:38 a.m.