Individual genotype statistics for an R/qtl cross object

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

Usage

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

Arguments

cross: An R/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 both. "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.

Details

This function is used in profileGen to plot any combination of returned linkage map statistics on a single graphical display.

Value

A list with elements named by the stat.type used in the call. If bychr = TRUE then each element is a data frame of statistics with columns named by the linkage groups. If bychr = FALSE then each element is a vector of statistics named by the stat.type.

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")

## produce all genotype crossover and double crossover statistics

sg <- statGen(mapDH, stat.type = c("xo","dxo"))