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

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

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")

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(ASMap)
Loading required package: qtl
Loading required package: gtools
Loading required package: fields
Loading required package: spam
Loading required package: grid
Spam version 1.3-0 (2015-10-24) is loaded.
Type 'help( Spam)' or 'demo( spam)' for a short introduction 
and overview of this package.
Help for individual functions is also obtained by adding the
suffix '.spam' to the function name, e.g. 'help( chol.spam)'.

Attaching package: 'spam'

The following objects are masked from 'package:base':

    backsolve, forwardsolve

Loading required package: maps

 # maps v3.1: updated 'world': all lakes moved to separate new #
 # 'lakes' database. Type '?world' or 'news(package="maps")'.  #


Loading required package: RColorBrewer
Loading required package: lattice
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/ASMap/profileMark.Rd_%03d_medium.png", width=480, height=480)
> ### Name: profileMark
> ### Title: Profile individual marker and interval statistics for an R/qtl
> ###   cross object
> ### Aliases: profileMark
> ### Keywords: misc
> 
> ### ** Examples
> 
> 
> data(mapDH, package = "ASMap")
> 
> ## profile chosen statistics
> 
> profileMark(mapDH, stat.type = c("seg.dist","prop","erf"), layout =
+       c(1,4), type = "l")
Warning message:
In summary.cross(cross) :
  Some markers at the same position on chr 1B1,1D,2B,2D1,3A,3B,3D,4A,5A,5B,5D,6D,7A,7B,7D; use jittermap().
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>