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 |
... |
further arguments for function |
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
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 | ## 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)
|
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