profileGen {ASMap} | R Documentation |
Profile individual genotype statistics for the current linkage map order of and R/qtl cross object
profileGen(cross, chr, bychr = TRUE, stat.type = c("xo", "dxo",
"miss"), id = "Genotype", xo.lambda = NULL, ...)
cross |
An qtl |
chr |
Character vector of linkage group names used for subsetting the linkage map. |
bychr |
Logical vector determining whether statistics should be plotted by chromosome (see Details). |
stat.type |
Character string of any combination of |
id |
Character string determining the column of |
xo.lambda |
A numerical value for the expected rate of recombination. (see Details). |
... |
Other arguments to be passed to the high level lattice plot. |
This function uses statGen
to profile statistics for the
genotypes for the current order of the linkage map. Any combination of
"xo"
or "dxo"
or "miss"
may be given to
simultaneous plot. If bychr = TRUE
then the plots will be further partitioned by
linkage groups given by chr
.
If a numerical value is given for xo.lambda
then the
recombination count for each genotype is tested against the expected
recombination rate xo.lambda
using a simple one-tailed test of a
Poisson mean. Any lines that have a p-value less than than a family wise
error rate based on bonferroni adjustment of the usual alpha level of 0.05 are
annotated on the profiles being plotted.
A lattice panel plot with panels described by the stat.type
given
in the call and genotype statistics are returned invisibly. If
xo.lambda
is not NULL then these statistics also include a
logical vector named "xo.lambda"
that is returned from testing
the individuals for inflated recombination rates (see Details).
Julian Taylor
Taylor, J., Butler, D. (2017) R Package ASMap: Efficient Genetic Linkage Map Construction and Diagnosis. Journal of Statistical Software, 79(6), 1–29.
data(mapDH, package = "ASMap")
## profile all genotype crossover and double crossover statistics
profileGen(mapDH, bychr = FALSE, stat.type = c("xo","dxo"),
xo.lambda = 25, layout = c(1,3))