Description Usage Arguments Details Author(s) References Examples
Generate an image of the local intensity average
1 2 3 |
int |
a |
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 |
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.
Jacques Rougemont, Arnaud Amzallag, Christian Iseli, Laurent Farinelli, Ioannis Xenarios, Felix Naef
Probabilistic base calling of Solexa sequencing data, BMC Bioinformatics 2008, 9:431
1 2 3 4 5 6 7 8 9 10 11 | 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)
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