updated: comments and sanity checks

Author: filippob

introduction_to_animal_breeding/notebooks/8.gwas_basic_models.Rmd

@@ -125,7 +125,7 @@ load("../data/pca.RData")
 names(res)
 
 npcs = length(res$sdev)
-print(paste("The total number of PCs is", npcs, ": can you guess why?"))
+print(paste("QUESTION: The total number of PCs is", npcs, ": can you guess why?"))
 ```
 
 #### Eigenvalues
@@ -145,7 +145,7 @@ sum(variance[c(1:3)])
 
 ```{r echo=TRUE}
 library("factoextra")
-fviz_eig(res, ncp = 50)
+fviz_eig(res, ncp = 25)
 ```
 
 #### Use principal components to model population structure
@@ -212,6 +212,10 @@ phenotypes <- phenotypes[phenotypes$id %in% genotypes$IID,]
 phenotypes <- phenotypes[,c(1,3)]
 ```
 
+```{r}
+head(phenotypes)
+```
+
 ### Kinship matrix
 
 We saw that one option to account for population structure in the GWAS