binSet: Apply bins to peak tables, creating arrays of AFLP data
In plantarum/binner: Read fsa fragment files from an ABI Genetic Analzyer

Description Usage Arguments Details Value Author(s)

View source: R/binSet.R

Functions for converting peak tables to AFLP data arrays, and combining multiple arrays for analysis.

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binSet(pt, bins, pref, hthresh = 100)

aflpCombine(aflp1, aflp2)

`pt`	A peak table, as generated by `fsa2PeakTab`
`bins`	A bin table, as produced by `fsaRGbin`
`pref`	A prefix to append to bin names, to allow for later combining data from different primer pairs
`hthresh`	The height threshold to score peaks as 'present'. You can revisit this decision later in the process.
`aflp1`	aflp data arrays, as produced by `binSet`
`aflp2`	aflp data arrays, as produced by `binSet`

binSet takes a peak table, applies the given bins, and returns a 3D aflp data array.

aflpCombine takes two aflp data arrays, as produced from binSet, and combines them into a single array

binSet returns a 3D array. The rows are samples, the columns are fragments, and the third dimension splits the array into allele calls ("alleles"), peak heights ("heights") and fragment size in basepairs ("sizes"). Thus, to retrieve the presence/absence matrix of allele calls, use: aflp[ , , "alleles"], where aflp is the object returned by binSet.

Other data summaries are readily available by creative slicing and dicing of the 3D array.

Tyler Smith

plantarum/binner documentation built on May 25, 2019, 8:20 a.m.