Profile individual genotype statistics for an R/qtl cross object

Description

Profile individual genotype statistics for the current linkage map order of and R/qtl cross object

Usage

profileGen(cross, chr, bychr = TRUE, stat.type = c("xo", "dxo", "miss"),
           id = "Genotype", xo.lambda = NULL, ...)

Arguments

Details

This function uses statGen to profile statistics for the genotypes for the current order of the linkage map. Any combination of "xo" or "dxo" or "miss" may be given to simultaneous plot. If bychr = TRUE then the plots will be further partitioned by linkage groups given by chr.

If a numerical value is given for xo.lambda then the recombination count for each genotype is tested against the expected recombination rate xo.lambda using a simple one-tailed test of a Poisson mean. Any lines that have a p-value less than than a family wise error rate based on bonferroni adjustment of the usual alpha level of 0.05 are annotated on the profiles being plotted.

Value

A lattice panel plot with panels described by the stat.type given in the call and genotype statistics are returned invisibly. If xo.lambda is not NULL then these statistics also include a logical vector named "xo.lambda" that is returned from testing the individuals for inflated recombination rates (see Details).

Author(s)

Julian Taylor

See Also

statGen

Examples

data(mapDH, package = "ASMap")

## profile all genotype crossover and double crossover statistics

profileGen(mapDH, bychr = FALSE, stat.type = c("xo","dxo"),
     xo.lambda = 25, layout = c(1,3))

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)

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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/profileGen.Rd_%03d_medium.png", width=480, height=480)
> ### Name: profileGen
> ### Title: Profile individual genotype statistics for an R/qtl cross object
> ### Aliases: profileGen
> ### Keywords: misc
> 
> ### ** Examples
> 
> 
> data(mapDH, package = "ASMap")
> 
> ## profile all genotype crossover and double crossover statistics
> 
> profileGen(mapDH, bychr = FALSE, stat.type = c("xo","dxo"),
+      xo.lambda = 25, layout = c(1,3))
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>