Individual marker and interval statistics for an R/qtl cross object
statMark(cross, chr, stat.type = c("marker","interval"),
map.function = "kosambi")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.
An qtl cross object with class structure "bc",
"dh", "riself", "bcsft". (see ?mstmap.cross for more details.)
Character vector of linkage group names used for subsetting the linkage map.
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).
Character string of either "koasmbi", "haldane",
"morgan" or "cf" defining the map
function to be used for interval related statistics.
Julian Taylor
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.
Taylor, J., Butler, D. (2017) R Package ASMap: Efficient Genetic Linkage Map Construction and Diagnosis. Journal of Statistical Software, 79(6), 1--29.
profileMark
data(mapDH, package = "ASMap")
## produce all statistics
sm <- statMark(mapDH, stat.type = c("marker","interval"))
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