eset_pca.R

# Performs principal components analysis on an ExpressionSet
eset_pca <- function (eset) {
  mypca <- prcomp(t(na.omit(exprs(eset))))
  pca <- as.data.frame(mypca$x)
  pc1var <- round(summary(mypca)$importance[2,1]*100, digits<-1)
  pc2var <- round(summary(mypca)$importance[2,2]*100, digits<-1)
  pc1lab <- paste0("PC1 (",as.character(pc1var),"%)")
  pc2lab <- paste0("PC1 (",as.character(pc2var),"%)")
  out <- merge(pData(eset), pca, by<-"row.names") %>% 
    dplyr::rename(id<-Row.names)
  attr(out, "pc1lab") <- pc1lab
  attr(out, "pc2lab") <- pc2lab
  out
}