profileMark {ASMap}

Profile individual marker and interval statistics for an R/qtl cross object

Description

Graphically profile individual marker and interval statistics for an R/qtl cross object

Usage

profileMark(cross, chr, stat.type = "marker", use.dist = TRUE,
          map.function = "kosambi", crit.val = NULL,
          display.markers = FALSE, mark.line = FALSE, ...)

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.

stat.type

Character string of either "marker" or "interval" or both. Also this can be a set of character strings relating to individual marker or interval statistics that want to be viewed simultaneously (see Details).

use.dist

Logical value determining whether the actual map distances should be use to represent marker positions. If FALSE then markers are placed equidistant from each other.

map.function

Character string of either "koasmbi", "haldane", "morgan" or "cf" defining the map function to be used for interval related statistics.

crit.val

The critical value to be used in displaying marker or intervals above a certain threshold (see Details).

display.markers

A logical value determining whether marker names should be displayed on the bottom axis.

mark.line

A logical value determining whether vertical lines should be drawn at marker positions. This may be useful to line up marker positions across several plots.

...

Other arguments to be passed to the high level lattice plot.

Details

This graphical function calls the function statMark to retrieve marker and interval statistics. If "marker" is given as the stat.type then the complete set of marker statistics is plotted simultaneously. If "interval" is given as the stat.type then the function simultaneously plots the complete set of interval statistics. Both can also be chosen.

This function also allows users to choose any combination of marker or interval statistics they would like to view. The set of available marker statistics that can be profiled are given below

• "seg.dist": Profile the -log10 p-value. results from a test of segregation distortion for each marker.

• "miss": Profile the proportion of missing values for each marker.

• "prop": Profile the allele proportions for each marker.

• "dxo": Profile the number of double crossovers occurring at each marker.

The set of available interval statistics that can be profiled are given below

• "erf": Profile the recombination fractions for the intervals.

• "lod": Profile the LOD score for the test of no linkage between markers in an interval.

• "dist": Profile the interval map distance taken from the map component of each linkage group.

• "mrf": Profile the map recombination fraction for the intervals.

• "recomb": Profile the actual number of recombinations within each of the intervals.

If crit.val="bonf" and marker statistics are plotted then any markers that have p-value for the test of segregation distortion less than the family wise error rate based on a bonferroni adjustment of the usual 0.05 alpha level, are annotated on each of the marker plots. If any interval statistics are being plotted then any intervals that have a p-value for the test of no linkage that is less than a bonferroni adjustment of the usual 0.05 alpha level are annotated on each of the interval statistics plots.

Value

A lattice panel plot is displayed with panels described by the stat.type given in the call and the complete marker/interval statistics are returned invisibly. If crit.val is not NULL then both the marker/interval statistics are returned with an extra logical column called "crit.val" from testing markers for segregation distortion and intervals for weak linkage (see Details).

Author(s)

Julian Taylor

References

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

See Also

profileMark

Examples

data(mapDH, package = "ASMap")

## profile chosen statistics

profileMark(mapDH, stat.type = c("seg.dist","prop","erf"), layout =
      c(1,4), type = "l")