I'm looking into using exomeDepth R package for CNV analysis; however, I have a couple questions from reading the manual (https://cran.r-project.org/web/packages/ExomeDepth/vignettes/ExomeDepth-vignette.pdf) regarding building the reference set (page.5)
Here is what the manual suggested:
my.matrix <- as.matrix( ExomeCount.dafr[, my.choice$reference.choice, drop = FALSE]) my.reference.selected <- apply(X = my.matrix, MAR = 1, FUN = sum)
In this test case there are 3 samples selected as the appropriate reference set. Why did they use FUN = sum instead of FUN = mean? Wouldn't that make the reference set counts a lot higher than the test set counts?
The other question is regarding the reference set selection - it looks like from the manual all the samples other than the one being tested gone through the function select.reference.set . However, if I have 14 cancer samples and 2 normal samples - shall I only input 2 normal samples to select.reference.set ? Or shall I use all the 15 samples that is not the current tested one?