defineBins: Define bins in AFLP object
In AFLP: Analysis of AFLP data

Description Usage Arguments Details Value Author(s) References See Also

This function is only relevant when the AFLP object contains raw data of peak values.

1 2	defineBins(dataset, minPeakHeight, minBinWidth = 1, maxBinWidth = 5, missingPeakRatio = 0.8)

`dataset`	An AFLP object
`minPeakHeight`	If set, only peaks with at least this amount of RFU will be taken into account when defining bins.
`minBinWidth`	Bins wider that this minimum AND who have at least one replicate with more than one peak in that bin, will be split into to smaller bins.
`maxBinWidth`	If a bin is wider than this number of basepairs, then the algorithm will split the bin, regardless the number of peaks within each replicate.
`missingPeakRatio`	If no peak is found for a give bin and given replicate, then a peak value will be given that is equal to mssingPeakRatio times the lowest peak value in the dataset.

The peaks are aggregated into bins according to the algoritme described by Arrigo et al (2009) Arrigo2009.

A new AFLP object were the fluorescence slot is replaced by the bins.

Thierry Onkelinx Thierry.Onkelinx@inbo.be, Paul Quataert

Arrigo, N., Tuszynski, J., Ehrich, D., Gerdes, T. and Alvarez, N. (2009), Evaluating the impact of scoring parameters on the structure of intra-specific genetic variation using RawGeno, an R package for automating AFLP scoring. BMC Bioinformatics, 10:33, 10.1186/1471-2105-10-33, http://www.biomedcentral.com/1471-2105/10/33

normalise, readABI

AFLP documentation built on May 2, 2019, 6:13 p.m.