rawgenoBin: Locate bins using the RawGeno algorithm
In plantarum/binner: Read fsa fragment files from an ABI Genetic Analzyer

Description Usage Arguments Details Value Author(s) References Examples

fsaRGbin identifies bins in a peak table

1 2	fsaRGbin(pt, start = 49.999, end = 495, mxbin = 1.5, mnbin = 1, verbose = FALSE)

`pt`	a peak table, as produced by `fsa2PeakTab`

fsaRGbin calculates bins using all peaks in a peak table, including very small ones. As a consequence, some bins may include only peaks < 50 rfus, and will therefore appear to be 'empty' in scanGel(). These empty bins should be filtered out before analysis, and are not otherwise of any concern.

Note that the way the algorithm is coded, the largest bin will always be bounded on the upper side by 495. Consequently, this bin may appear quite large. It will only ever include fragments that are collectively within mxbin base pairs of each other, but may include a sizeable empty section above the actual fragments. Again, this is not a concern for subsequent analysis.

TBA

Tyler Smith

This function uses the ‘RawGeno’ binning algorithm of Arrigo et al. 2009. I reimplemented this following their flow-chart, rather than directly copying the code in the RawGeno package. As a consequence, there may be some small numerical differences between the two implementations. I elected not to copy the code as the style of the two packages are not easily reconciled.

Arrigo, N., Tuszynski, J. W., Ehrich, D., Gerdes, T., & 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(1), 33.