gpData2cross: Conversion between objects of class 'cross' and 'gpData'
In synbreed: Framework for the Analysis of Genomic Prediction Data using R

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

Function to convert an object of class gpData to an object of class cross (F2 intercross class in the package qtl) and vice versa. If not done before, function codeGeno is used for recoding in gpData2cross.

1	gpData2cross(gpData, ...)

`gpData`	object of class `gpData` with non-empty elements for `pheno`, `geno` and `map`
`...`	further arguments for function `codeGeno`. Only used in `gpData2cross`.

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.

Object of class cross of gpData for function gpData2cross and cross2gpData, respectively.

Valentin Wimmer and Hans-Juergen Auinger

Broman, K. W. and Churchill, S. S. (2003). R/qtl: Qtl mapping in experimental crosses. Bioinformatics, (19):889-890.

create.gpData, read.cross , codeGeno

## 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)


# from cross to gpData
data(fake.f2)
fake.f2.gpData <- cross2gpData(fake.f2)
summary(fake.f2.gpData)

## End(Not run)