Last data update: 2014.03.03
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R: Rolexa Setup Class
RolexaRun-class | R Documentation |
Rolexa Setup Class
Description
A class holding parameters for subsequent run of Rolexa algorithms
Slots
MinimumTagLength tags shorter than this will not be saved (15)
SequencingLength number of cycles of sequencing, used to calculate the number of columns in files (36)
Barcode number of bases used as barcode at the beginning of the tag (0)
HThresholds entropy thresholds between 1 and 2-base ambiguities, 2 and 3-base ambiguities and 3-base ambiguity or undecided (log2(c(1.5,2.5,3.5)))
IThresholds total entropy thresholds, as a function of tag length (log2(4+1:36/6))
PET paired-end sequencing run (FALSE)
fit use full EM convergence instead of only one-step
optimization (FALSE)
normal use tile-level normalization before
base-calling (TRUE)
decorrelate use 'cycle'-level decorrelation procedure,
'channel'-level, 'both' or 'none' ('both')
idsep character separating coordinate fields in
sequence headers (":")
verbose print debug information if >0 (0)
colors list of colors to use in the plots
These values are set using SetModel and a list of the slot
values can be retrieved with GetModel .
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
See Also
DeCorrelateChannels , DeCorrelateCycles , and TileNormalize
Results
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