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

Description

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

Usage

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

Arguments

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.

Author(s)

Julian Taylor

See Also

profileMark

Examples

data(mapDH, package = "ASMap")

## produce all statistics

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

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/statMark.Rd_%03d_medium.png", width=480, height=480)
> ### Name: statMark
> ### Title: Individual marker and interval statistics for an R/qtl cross
> ###   object
> ### Aliases: statMark
> ### Keywords: misc
> 
> ### ** Examples
> 
> 
> data(mapDH, package = "ASMap")
> 
> ## produce all statistics
> 
> sm <- statMark(mapDH, stat.type = c("marker","interval"))
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>