Description Usage Arguments Details Value Author(s) References Examples

Model-based classification of intensity data points, to either perform a base calling or generate diagnostic plots

1 2 3 |

`run` |
a |

`int` |
a |

`seqInit` |
a |

`colonies` |
which colonies to select |

`cycles` |
which cycles to select |

`plot` |
if TRUE do a plot rather then perform a base-calling |

`...` |
additional arguments, ignored |

This will use the EEV model of mclust to fit the
data clouds with a mixture of 4 gaussian distributions.
and generate a list of tags and
entropy scores for each sequenced colony (if `plot`

is FALSE) or
plots two 2-dimensional projections for each selected
cycle with gaussian parameters represented by standard ellipses and data
points colored according to the induced classification.

If `fit`

is TRUE, then the
EM algorithm is run to convergencce, otherwise only
an E-step and an M-step
are performed to evaluate the probabilities.

The fitting procedure then uses
`HThresholds`

to decide if a base is
unambiguous and if degenerate IUPAC codes will be used.

if `plot`

is FALSE, `SeqScore`

returns a list with an
`id`

slot containing the colonies coordinates, an
`sread`

slot which is a `DNAStringSet`

object and an `entropy`

matrix

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 | ```
path = SolexaPath(system.file("extdata", package="ShortRead"))
rolenv = SetModel(idsep="_")
int = readIntensities(path,pattern="s_1_0001",withVariability=FALSE)
seq = CombineReads(run=rolenv,path=path,pattern="s_1_0001_seq*")
results = SeqScore(run=rolenv,int=int,seqInit=seq,cycles=1:10)
results$sread
``` |

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

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