Individual marker and interval statistics for an R/qtl cross object

Usage

statMark(cross, chr, stat.type = c("marker","interval"),
         map.function = "kosambi")

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.
stat.type: Character string of either "marker" or "interval" or both. "marker" produces individual marker related statistics and "interval" produces interval related statistics for the current map order (see Details).
map.function: Character string of either "kosambi", "haldane", "morgan" or "cf" defining the map function to be used for interval related statistics.

Details

If "marker" is chosen then a call to geno.table from qtl is used to return individual marker statistics for segregation distortion, as well as allele and missing value proportions. For the current map order the number of double crossovers at each marker are also returned.

If "interval" is chosen then interval statistics are returned for the current map order. These include the estimated recombination fraction and LOD score between adjacent markers, calculated from est.rf in qtl. Also returned are the map interval distances and converted map recombination fractions extracted from the "map" component of each linkage group as well as the actual number of recombinations between markers.

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

Value

A list named by the stat.type used in the call. Each element is a data frame of statistics with columns named by the statistic.

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 statistics

sm <- statMark(mapDH, stat.type = c("marker","interval"))