Rolexa (version 1.28.0)

TileImage: Reconstruct tile image

Description

Generate an image of the local intensity average

Usage

"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.

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=readIntensityInfo(int)$tile[1],channel=c,ncell=5)
int2 = TileNormalize(rolenv,int=int,cycles=1)
x11()
par(mfrow=c(2,2))
for (c in c('A','C','G','T'))
    TileImage(int=int2,cycle=1,tile=readIntensityInfo(int)$tile[1],channel=c,ncell=5)