DO_Recla2

Diversity Outcross data from Recla et al (2019)

Source

• Phenotype data from https://phenome.jax.org/projects/Recla2
• Genotype data from https://dodb.jax.org (Carol Bult, Genetic mapping in Diversity Outbred mice identifies a Trpa1 variant influencing late...)

The genotype data were subset to the 275 mice for which phenotype data was available, and to the markers with mapped locations in the revised MegaMUGA annotations at https://github.com/kbroman/MUGAarrays. There were 83 markers missing from the genotype data, so the available data is the subset of 74,906 MegaMUGA markers that map to chr 1-19 or X and are present in the data.

Files

• recla2.json - Control file in JSON format
• recla2_covar.csv - covariate data (individuals x covariates)
• recla2_pheno.csv - phenotype data (individuals x phenotypes)
• recla2_geno.csv - genotype data (markers x individuals)
• recla2_foundergeno.csv - founder genotype data (markers x founders)
• recla2_gmap.csv - Genetic map of markers (positions in cM)
• recla2_pmap.csv - Physical map of markers (positions in NCBI38/mm10 Mbp)

The data are also available as a zip file, recla2.zip.

File format

See the R/qtl2 input file format.

Citations

Recla JM, Bubier JA, Gatti DM, Ryan JL, Long KH, Robledo RF, Glidden NC, Hou G, Churchill GA, Maser RS, Zhang ZW, Young EE, Chesler EJ, Bult CJ (2019) Genetic mapping in Diversity Outbred mice identifies a Trpa1 variant influencing late-phase formalin response. Pain 160:1740-1753 doi:10.1097/j.pain.0000000000001571

Use with R/qtl2

Load these data into R directly from the web as follows:

library(qtl2)
file <- paste0("https://raw.githubusercontent.com/rqtl/",
               "qtl2data/master/DO_Recla2/recla2.zip")
recla2 <- read_cross2(file)