targetregion: Description of the targetregion data set

In hsrecombi: Estimation of Recombination Rate and Maternal LD in Half-Sibs

Description of the targetregion data set

Description

The data set contains sire haplotypes, assignment of progeny to sire, progeny genotypes and physical map information in a target region

The raw data can be downloaded at the source given below. Then, executing the following R code leads to the data provided in targetregion.RData.

hapSire

matrix of sire haplotypes of each sire; 2 lines per sire; 1. column contains sireID

daughterSire

vector of sire ID for each progeny

genotype.chr

matrix of progeny genotypes

map.chr

SNP marker map in target region

Source

The data are available at RADAR \Sexpr[results=rd]{tools:::Rd_expr_doi("10.22000/280")}

Examples

## Not run: 
# download data from RADAR (requires about 1.4 GB)
url <- "https://www.radar-service.eu/radar-backend/archives/fqSPQoIvjtOGJlav/versions/1/content"
curl_download(url = url, 'tmp.tar')
untar('tmp.tar')
file.remove('tmp.tar')
path <- '10.22000-280/data/dataset'
## list of haplotypes of sires for each chromosome
load(file.path(path, 'sire_haplotypes.RData'))
## assign progeny to sire
daughterSire <- read.table(file.path(path, 'assign_to_family.txt'))[, 1]
## progeny genotypes
X <- as.matrix(read.table(file.path(path, 'XFam-ARS.txt')))
## physical and approximated genetic map
map <- read.table(file.path(path, 'map50K_ARS_reordered.txt'), header = T)
## select target region
chr <- 1
window <- 301:500
## map information of target region
map.chr <- map[map$Chr == chr, ][window, ]
## matrix of sire haplotypes in target region
hapSire <- rlist::list.rbind(haps[[chr]])
sireID <- 1:length(unique(daughterSire))
hapSire <- cbind(rep(sireID, each = 2), hapSire[, window])
## matrix of progeny genotypes
genotype.chr <- X[, map.chr$SNP]
colnames(genotype.chr) <- map.chr$SNP
save(list = c('genotype.chr', 'hapSire', 'map.chr', 'daughterSire'),
     file = 'targetregion.RData', compress = 'xz')

## End(Not run)

hsrecombi documentation built on June 7, 2023, 6:02 p.m.