germ: Compute matches for RFLP data via GERM.

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

View source: R/germ.R

Description

Compute matches for RFLP data using the Good-Enough RFLP Matcher (GERM) program.

Usage

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germ(newData, refData, parameters = list("Max forward error" = 25,
                                         "Max backward error" = 25,
                                         "Max sum error" = 100,
                                         "Lower measurement limit" = 100), 
     method = "joint", na.rm = TRUE)

Arguments

newData

data.frame with new RFLP data; see newDataGerm.

refData

data.frame with reference RFLP data; see refDataGerm.

parameters

list of the four program parameters of GERM; see details section.

method

matching and ranking method used for computation; see details section.

na.rm

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

Details

There are four matching and ranking methods which are "joint", "forward", "backward", and "sum". For more details see Dickie et al. (2003).

The parameters of the GERM software are: "Max forward error": Used if "matching and ranking method" is set to "forward" or "joint". "Max backward error": Used if "matching and ranking method" is set to "backward" or "joint". "Max sum error": Used for matching if "matching and ranking method" is set to "sum". "Lower measurement limit": The lower bound of measurements (often 100 or 50, depending on ladder used).

Value

A named list with the results.

Author(s)

Mohammed Aslam Imtiaz, Matthias Kohl Matthias.Kohl@stamats.de

References

Ian A. Dickie, Peter G. Avis, David J. McLaughlin, Peter B. Reich. Good-Enough RFLP Matcher (GERM) program. Mycorrhiza 2003, 13:171-172.

See Also

newDataGerm, refDataGerm

Examples

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  data(refDataGerm)
  data(newDataGerm)
  
  ## Example 1
  res1 <- germ(newDataGerm[1:7,], refDataGerm)
  
  ## Example 2
  res2 <- germ(newDataGerm[8:15,], refDataGerm)
  
  ## Example 3
  res3 <- germ(newDataGerm[16:20,], refDataGerm)
  
  ## all three examples in one step
  res.all <- germ(newDataGerm, refDataGerm)

Example output

Loading required package: RColorBrewer
Warning message:
In min(abs(y[i] - x)) : no non-missing arguments to min; returning Inf
Warning message:
In min(abs(y[i] - x)) : no non-missing arguments to min; returning Inf
Warning message:
In min(abs(y[i] - x)) : no non-missing arguments to min; returning Inf
Warning messages:
1: In min(abs(y[i] - x)) : no non-missing arguments to min; returning Inf
2: In min(abs(y[i] - x)) : no non-missing arguments to min; returning Inf
3: In min(abs(y[i] - x)) : no non-missing arguments to min; returning Inf

RFLPtools documentation built on May 4, 2021, 1:06 a.m.