profileMark {ASMap}  R Documentation 
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 
chr 
Character vector of linkage group names used for subsetting the linkage map. 
stat.type 
Character string of either 
use.dist 
Logical value determining whether the actual map distances should be use
to represent marker positions. If 
map.function 
Character string of either 
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 pvalue. 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 pvalue 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 pvalue 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
Examples
data(mapDH, package = "ASMap")
## profile chosen statistics
profileMark(mapDH, stat.type = c("seg.dist","prop","erf"), layout =
c(1,4), type = "l")