RFLPdist2ref: Compute distance between RFLP data and RFLP reference data.
In RFLPtools: Tools to analyse RFLP data

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

Function to compute distance between RFLP data and RFLP reference data.

1	RFLPdist2ref(x, ref, distfun = dist, nrBands, LOD = 0)

`x`	data.frame with RFLP data; e.g. `RFLPdata`.
`ref`	data.frame with RFLP reference data; e.g. `RFLPref`.
`distfun`	function computing the distance with default `dist`; cf. `dist`.
`nrBands`	only samples and reference samples with this number of bands are considered.
`LOD`	threshold for low-bp bands.

For each sample with nrBands bands the distance to each reference sample with nrBands bands is computed. The result is a matrix with the corresponding distances where rows represent the samples and columns the reference samples.

If LOD > 0 is specified, all values below LOD are removed before the distances are calculated. This applies to x and ref.

A matrix with distances.

Fabienne Flessa Fabienne.Flessa@uni-bayreuth.de,
Alexandra Kehl Alexandra.Kehl@botgarten.uni-tuebingen.de,
Matthias Kohl Matthias.Kohl@stamats.de

Flessa, F., Kehl, A., Kohl, M. Analysing diversity and community structures using PCR-RFLP: a new software application. Molecular Ecology Resources 2013 Jul; 13(4):726-33.

RFLPdata, dist

## Euclidean distance
data(RFLPdata)
data(RFLPref)
nrBands(RFLPref)
RFLPdist2ref(RFLPdata, RFLPref, nrBands = 4)
RFLPdist2ref(RFLPdata, RFLPref, nrBands = 6)

Dir <- system.file("extdata", package = "RFLPtools") # input directory 
filename <- file.path(Dir, "AZ091016_report.txt")
RFLP1 <- read.rflp(file = filename)
RFLP2 <- RFLPqc(RFLP1)
nrBands(RFLP2)
RFLPdist2ref(RFLP1, RFLPref, nrBands = 4)
RFLPdist2ref(RFLP1, RFLPref, nrBands = 5)