Simulated dataset for the "Profile of Causative SNP" manuscript

Description

The data for this study were simulated using the AlphaSimR package (Faux et al. 2016; Gaynor et al. 2019) and run using R version 3.4.4 (R Core Team). Parameter files for analyses using the BLUPF90 family of software (Misztal et al. 2014) are included.

The dataset is split into three directories (NE60, NE60_3x, and NE600) corresponding to three different scenarios based on different effective population sizes and different numbers of individuals.

Each directory consists of the following files:

01_renumf90.par (parameter file for running renumf90)

02_blupf90.par (parameter file for running blupf90)

03_postGSf90.par (parameter file for running postGSf90)

chrmap.dat (SNP map file in BLUPF90 format)

markers.dat (SNP genotypes in BLUPF90 format)

pedigree.txt (pedigree in BLUPF90 format)

phenotype.txt (phenotypic data in BLUPF90 format)

The initial AlphaSimR script is included (InitialASR/initial_data_simulator.R)

Software

R is available at https://www.r-project.org

AlphaSimR is available as R package https://cran.r-project.org/web/packages/AlphaSimR/index.html

BLUPF90 family of software (renumf90, blupf90, and postGSf90) are available at http://nce.ads.uga.edu/software/