PCA plot of extracted methylation values — PCA • DMRichR

Performs and plots a PCA from individual smoothed methylation values

Usage

PCA(
  matrix = matrix,
  testCovariate = testCovariate,
  bs.filtered.bsseq = bs.filtered.bsseq
)

Arguments

matrix: A matrix of smoothed individual methylation values
testCovariate: Factor of interest
bs.filtered.bsseq: Smoothed bsseq object with a testCovariate in pData

Value

A ggplot object that can be viewed by calling it, saved with ggplot2::ggsave(), or further modified by adding ggplot2 syntax

Details

PCA

References

https://stackoverflow.com/questions/40315227/how-to-solve-prcomp-default-cannot-rescale-a-constant-zero-column-to-unit-var/40317343