posted on 2019-10-18, 16:17authored byLuke BrowneLuke Browne, Jessica W. Wright, Sorel Fitz-Gibbon, Paul F. Gugger, Victoria L. Sork
Phenotypic, genotype, and analysis scripts for "Adaptational lag to temperature in valley oak (Quercus lobata) can be mitigated by genome-informed assisted gene flow"
Main growth analysis of the 5,051 seedlings can be reproduced by running the "04a-fit-full-model.R" script and loading the "full growth analysis.Rdata" dataset in R
Data for GEBV estimation with cross-validation not across families is contained within the directories in: run_642454_tmax_sum_dif_rgr_10fold_notacross_seed300.zip
Data for GEBV estimation with cross-validation across families is in: run_648224_tmax_sum_dif_rgr_10fold_acrossfams_seed300.zip
To reproduce the GEBV estimation and analysis, download the corresponding zip files that contains the R environment and datasets and use the "04d-analyze-models-cluster.R" script
"valley oak growth data - all seedlings.csv" contains the relative growth rates and relevant covariates for the 5,051 seedlings in an easy to read format
"gbs451_FIL-4_noLD.recode.vcf" contains the genotypes of each maternal tree in the study in VCF format