simMixMerlin: A DNA mixture is generated from individual genotypes using...

In euroMixR: Calculations for DNA mixtures, only R code

Description

A linkdat object is created. MERLIN files can be generated or mixtures can be generated based on existing files. This function requires MERLIN to be installed and correctly pointed to in the PATH environment variable.

Usage

simMixMerlin(x, aa, afreq, generate = FALSE)

Arguments

x	linkdat object
aa	allele list. aa[[1]] contains alleles for marker 1. MERLIN has an upper limit on the number of alleles therefore has problems with one marker, SE33, in db.
afreq	Frequency list
generate	If TRUE, Merlin files are generated

Value

y	linkdat object
comp2	list of mixtures

Author(s)

Thore Egeland <[e-mail]>

Examples

## Not run: 
#Example 1
require(paramlink)
data(db)
x=cousinPed(1)
x=swapSex(addOffspring(x,father=7,mother=8,noff=2),ids=10)
db2=split(db,db$Marker)
Nmarkers=5
aa=vector("list",Nmarkers)
afreq=vector("list",Nmarkers)
for (i in 1:Nmarkers){
aa[[i]]=db2[[i]]$Allel
afreq[[i]]=db2[[i]]$Frequency
m=marker(x,9,c(1,1),10,c(1,1),alleles=1:length(aa[[i]]),afreq=afreq[[i]])
x=addMarker(x,m)
}
res=simMixMerlin(x,aa,afreq,generate=TRUE)
#The map file generated default above leads to tightly linked markers. The map file
#can be edited and simMixMerlin rerun with generate=FALSE. 
#Example 2 
#Next we consider an example #with two markers (for simplicity), D12 and VWA, markers 3 and 23 in db and illustrate
#how the map file is edited to account for linkage
x=cousinPed(1)
x=swapSex(addOffspring(x,father=7,mother=8,noff=2),ids=10)
Nmarkers=2
aa=vector("list",Nmarkers)
afreq=vector("list",Nmarkers)
i=0
for (j in c(3,23)){
i=i+1
aa[[i]]=db2[[i]]$Allel
afreq[[i]]=db2[[i]]$Frequency
m=marker(x,9,c(1,1),10,c(1,1),alleles=1:length(aa[[i]]),afreq=afreq[[i]])
x=addMarker(x,m)
}
res=simMixMerlin(x,aa,afreq,generate=TRUE)
#Next edit map file, normally this is done  simpler than below
map=read.table("merlin.map",header=FALSE)
map[,1]=c(12,13)
map[,3]=c(0.5,0.5)
write.table(map,"merlin.map",col.names=FALSE,quote=FALSE,row.names=FALSE)
res=simMixMerlin(x,aa,afreq,generate=FALSE)

## End(Not run)

euroMixR documentation built on May 2, 2019, 4:54 p.m.