Download Package `synbreed`

gpData2cross
21
Arguments
gpData
object of class gpData with non-empty elements for pheno, geno and map
cross
object of class cross
...
further arguments for function codeGeno. Only used in gpData2cross.
Details
In cross, genotypic data is splitted into chromosomes while in gpData genotypic data comprises all
chromosomes because separation into chromosomes in not required for genomic prediction. Note
that coding of genotypic data differs between classes. In gpData, genotypic data is coded as the
number of copies of the minor allele, i.e. 0, 1 and 2. Thus, function codeGeno should be applied to
gpData before using gpData2cross to ensure correct coding. In cross, coding for F2 intercross is:
AA = 1, AB = 2, BB = 3. When using gpData2cross or cross2gpData, resulting genotypic data
has correct format.
Value
Object of class cross of gpData for function gpData2cross and cross2gpData, respectively.
Author(s)
Valentin Wimmer and Hans-Juergen Auinger
References
Broman, K. W. and Churchill, S. S. (2003). R/qtl: Qtl mapping in experimental crosses. Bioinformatics, (19):889-890.
See Also
create.gpData, read.cross , codeGeno
Examples
## Not run:
library(synbreedData)
# from gpData to cross
data(maize)
maizeC <- codeGeno(maize)
maize.cross <- gpData2cross(maizeC)
# descriptive statistics
summary(maize.cross)
plot(maize.cross)
# use function scanone
maize.cross <- calc.genoprob(maize.cross, step=2.5)
result <- scanone(maize.cross, pheno.col=1, method="em")
# display of LOD curve along the chromosome
plot(result)