Data, R scripts and ASReml scripts

################################################################################################ # OBJECTIVE: Procedure to perform the data handling and the analyses + details about the files # # AUTHOR: Nicolas Bedere ([e-mail]) # # LICENCE: CC0 1.0 Universal (CC0 1.0), Public Domain Dedication # # LAST UPDATE: 2023-01-06 # # PLATFORM: x86_64-pc-linux-gnu (64-bit) # ################################################################################################ #### INTRODUCTION #### This text files aims to explain the procedure to perform both the data handling and the analyses in the paper: #### Description of the files: #1. Datasets PhenoAsreml.txt contains the observed values for the phenotypes described in the paper PhenoAsreml_scaled.txt contains the scaled (mean of zero and standard deviation of one) of the same phenotypes. THIS DATASET IS USED FOR BIVARIATE ANALYSES WITH 2x2 STRATA PhenoAsreml_scaledLong.txt contains the same information, organized differently because the dataset is reshaped from wide to long format. PhenoAsreml_scaledLong_3x3strata.txt contains the information for BackFat and BodyWeight, THIS DATASET IS USED FOR BIVARIATE ANALYSES WITH 3x3 STRATA PhenoAsreml_scaledLong_3x2strata.txt contains the information for BackFat and Adiponectin, THIS DATASET IS USED FOR BIVARIATE ANALYSES WITH 3x2 STRATA. It is only an example of dataset that needs to be generated in order to obtain all the results presented in the paper BEDERE_2023_Data_PedigreeHens.txt is the pedigree file (individual/sire/dam) traced back over 5 generations #2. Codes and parameter files BEDERE_2023_RScript_handlingdata_Long.R is an R code to reshape PhenoAsreml_scaled into PhenoAsreml_scaledLong and to subset it to generate PhenoAsreml_scaledLong_3x3strata for instance BEDERE_2023_ASREMLScript_bivariate_2x2strata.as (as well as ...3x2strata.as and ...3x3strata.as) are ASReml parameter files used to state the data, model specification and post-hoc calculation to ASReml Please, note that some variance components have been fixed in some analyses when the algorithm was struggling to converge. BEDERE_2023_RScript_BartlettTest.R is an R code to perform the Bartlett test. #2. Results examples Some output files of ASReml are provided to give an example of results for each type of bivariate analysis. The .asr file is the log of the program, explaining how the program ran The .res file is describing the residuals The .pvc file describes the variance components and provides the genetic parameters with their associated standard errors.