Description Usage Arguments Details Value See Also Examples
A generic function to modify the genetic map defined in the
"hypredGenome"
object
1 2 3 | hypredNewMap(object, ...)
## S4 method for signature 'hypredGenome'
hypredNewMap(object, new.map)
|
object |
an object of a class that holds information on map
positions of loci, typically an |
new.map |
numeric vector with the map positions of all loci (marker and qtl) |
... |
Methods may require further arguments. |
Only the map positions can be changed, the length of the chromosomes, their number and the number of SNP and QTL per chromosome is not modified. There are some validity checks included to assure that the new map agrees with these parameters.
The vector given to new.map
holds the positions of all loci. So
if, for example, the number of chromosomes is three and the number of
loci per chromosome is 10, then new.map[1:10]
must contain the
map of chromosome 1, new.map[11:20]
the map of chromosome 2 and
new.map[21:30]
the mao of chromosome 3.
The postions must give the distance to the beginning of the chromosome, not the distance between adjacent loci!
If the object included SNP blocks, they will not be adapted! Instead all
slots referring to the blocks are set to NULL
and a warning is issued.
A "hypredGenome"
object, modified accordingly.
The function hypredGenome
which creates the original object.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 | ## one chromosome of length 1 M and 5 SNP
random_map <- hypredGenome(1, 1.0, 5)
## map positions are random
slot(random_map,"pos.snp")
## change to regular positions
change_map <- c(0.1, 0.2, 0.3, 0.4, 0.5)
regular_map <- hypredNewMap(random_map, change_map)
slot(regular_map,"pos.snp")
|
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