FragMatch {RFLPtools}

Compute matches for RFLP data via FragMatch.

Description

Compute matches for RFLP data using FragMatch - a program for the analysis of DNA fragment data.

Usage

FragMatch(newData, refData, maxValue = 1000, errorBound = 25,
          weight = 1, na.rm = TRUE)

Arguments

newData

data.frame with new RFLP data; see newDataGerm.

refData

data.frame with reference RFLP data; see refDataGerm.

maxValue

numeric: maximum value for which the error bound is applied. Can be a vector of length larger than 1.

errorBound

numeric: error bound corresponding to maxValue. Can be a vector of length larger than 1.

weight

numeric: weight for weighting partial matches; see details section.

na.rm

logical: indicating whether NA values should be stripped before the computation proceeds.

Details

A rather simple algorithm which consists of counting the number of matches where it is considered a match if the value is inside a range of +/- errorBound.

If there is more than one enzyme, one can use weights to give the partial perfect matches for a certain enzyme a higher (or also smaller) weight.

Value

A character matrix with entries of the form "a_b" which means that there were a out of b possible matches.

Author(s)

Mohammed Aslam Imtiaz, Matthias Kohl [e-mail]

References

T. A. Saari, S. K. Saari, C. D. Campbell, I. J Alexander, I. C. Anderson. FragMatch - a program for the analysis of DNA fragment data. Mycorrhiza 2007, 17:133-136

See Also

newDataGerm, refDataGerm

Examples

  data(refDataGerm)
  data(newDataGerm)
  
  res <- FragMatch(newDataGerm, refDataGerm)