Eg9PP_Ganoderma

This repository contains the source R code to implement survival models presented in the paper "Identification of Ganoderma disease resistance loci using natural field infection of an oil palm multi-parent population" by [Sébastien Tisné] (https://www.researchgate.net/profile/Sebastien_Tisne) (CIRAD), Virginie Pomiès, Virginie Riou, Indra Syahputra, Benoît Cochard and Marie Denis for predicting spatial effects and mapping resistance QTL. R code was created by Marie Denis (CIRAD).

The project hence is currently funded, and the copyright owned, by [PalmElit] (http://www.palmelit.com/en/) and CIRAD. Document is under the CC BY-SA 4.0 license, and all R code are under the GNU AGPL v3.

R code:

1. call.R -- script to run R functions for predicting spatial effects and mapping resistance QTL on a real dataset
2. UtilFunctions.R -- functions called in Spatial and MappingQTL functions
3. Spatial.R -- function to predict spatial effects
4. MappingQTL.R -- function to map resistance QTL

Data:

1. KIN_Eg9PP_10.Rdata -- list of IBD matrices for the 10 first positions
2. Eg9PP_Phenotypes -- matrix with survival times, censoring indicators, and additional covariates for all palm trees
3. Eg9PP_Phenotypes_Mapping -- matrix with survival times, censoring indicators, and additional covariates for fully genotyped palm trees
4. Eg9PP_Pedigree: matrix with palm, father, and mother identifiers