Profile individual genotype statistics for an R/qtl cross object

Profile individual genotype statistics for the current linkage map order of and R/qtl cross object

Usage

profileGen(cross, chr, bychr = TRUE, stat.type = c("xo", "dxo",
           "miss"), id = "Genotype", xo.lambda = NULL, ...)

Arguments

cross: An qtl cross object with class structure "bc", "dh", "riself", "bcsft". (see ?mstmap.cross for more details.)
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 "xo" or "dxo" or "miss". "xo" calculates the number of crossovers, "dxo" calculates the number of double crossover and "miss" calculates the number of missing values.
id: Character string determining the column of cross$pheno that contains the genotype names.
xo.lambda: A numerical value for the expected rate of recombination. (see Details).
...: Other arguments to be passed to the high level lattice plot.

Details

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.

Value

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).

References

Taylor, J., Butler, D. (2017) R Package ASMap: Efficient Genetic Linkage Map Construction and Diagnosis. Journal of Statistical Software, 79(6), 1–29.

Author

Julian Taylor

Examples


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))