Fit and Plot intensities

Description

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

Usage

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

Arguments

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

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

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
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Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(Rolexa)
Error in library(Rolexa) : there is no package called 'Rolexa'
Execution halted