hsrecombi (version 1.0.1)

targetregion: 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

Examples

if (FALSE) {
# 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')
}