PCA

HIBLUP has the function of calculating PCA for a population, the genotype or the relationship matrix should be provided.

Calculating PCs from genotype

./hiblup --pca --bfile demo --out demo

Note that user can add flag --step n to control the memory cost, and specify flag --npc n to output several number of PCs instead of all.

Calculating PCs from XRM

./hiblup --pca --xrm demo.GA --npc 5 --out demo

There are two files demo.pc and demo.pcp will be generated.

The file demo.pc contains the calculated PCs, overview of the file:

id       PC1     PC2     PC3     PC4     PC5
IND0701  0.0413326       -0.00664808     -0.00795809     0.0218009       -0.0156735
IND0702  0.00856316      0.0378125       0.000503819     0.0205049       0.00972465
IND0703  -0.00793242     0.0458023       -0.00438572     -0.0173733      -0.0254701
IND0704  -0.00793248     0.0458023       -0.00438575     -0.0173733      -0.0254701

The file demo.pcp contains the Proportion and Cumulative Proportion of variance of PCs, overview of the file:

Components      PC1     PC2     PC3     PC4     PC5
Standard deviation      4.23976    4.10211    3.76024    3.66821    3.60725
Proportion of Variance  0.0224695  0.0210342  0.0176743  0.0168197  0.0162653
Cumulative Proportion   0.0224695  0.0435037  0.0611779  0.0779976  0.094263