Extract PCA score table

[Experimental] Compute variance explained by a few PCA axis

pca_scoretable(x, naxe = 1)

Arguments

x

glPCA object
naxe

number of axis for which you want to extract PCA scores

Details

PCA from glPca. It will return a dataframe, including ID and pca.score for the desire number of axis

Examples

## simulate a toy dataset
x <- adegenet::glSim(50,4e3, 50, ploidy=2)

#> Registered S3 method overwritten by 'spdep':
#>   method   from
#>   plot.mst ape 
## perform PCA
pca1 <- adegenet::glPca(x, nf=3)
## Extract variance
res <- pca_scoretable(pca1, naxe=3)
head(res)

#>   ID score.PC1  score.PC2  score.PC3
#> 1  1 -2.897836  2.7779365  2.4728657
#> 2  2 -1.921593 -2.4625237  1.0384473
#> 3  3 -1.747774 -2.0255692 -3.0321781
#> 4  4 -2.664595 -0.6764288  1.0973202
#> 5  5 -3.242396 -1.2912680  0.5102435
#> 6  6 -2.144298 -8.5077827  0.5113998