Model3: Fit and Plot intensities

Description Usage Arguments Details Value Author(s) References Examples

Description

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

Usage

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## S4 method for signature 'RolexaRun'
SeqScore(run=Rolexa.env,int,seqInit,colonies,cycles,plot=FALSE)
SeqScore(run,...)

Arguments

run

a RolexaRun object defining the run parameters

int

a SolexaIntensity object

seqInit

a ShortRead object

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

Details

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.

Value

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

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

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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.