Description Usage Arguments Details Value Author(s) References See Also Examples
Compute matches for RFLP data using the Good-Enough RFLP Matcher (GERM) program.
1 2 3 4 5 |
newData |
data.frame with new RFLP data; see |
refData |
data.frame with reference RFLP data; see |
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. |
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).
A named list with the results.
Mohammed Aslam Imtiaz, Matthias Kohl Matthias.Kohl@stamats.de
Ian A. Dickie, Peter G. Avis, David J. McLaughlin, Peter B. Reich. Good-Enough RFLP Matcher (GERM) program. Mycorrhiza 2003, 13:171-172.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 | 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)
|
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
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