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. Author manuscript; available in PMC: 2015 Apr 24.
Published in final edited form as: Curr Protoc Hum Genet. 2014 Apr 24;81:7.23.1–7.23.21. doi: 10.1002/0471142905.hg0723s81

Figure 8. Read depth projected in a principal component.

Figure 8

This principal component (the 3rd one, in this instance) has found the variance in read depth due to gender differences, with males having lower coverage on the X chromosome and higher coverage on the Y. Therefore, the loadings for this component have a correlation of 0.99 with the gender of the samples. Note that the R script creates the ‘PC’ sub-directory, which contains plots of the read depth data projected into each of the principal components: PC/PC.*.png.