Get CpG eigenvector scores from a principle component.
getPCRanks.Rd
Returns eigenvector scores for input CpG sites.
Arguments
- mat
Bismark2Matrix.R output file, or data frame object
- IDs
A character vector of IDs containing the common names for compared conditions. E.g., for samples trt1 & trt2 vs. ctl1 & ctl2, IDs=c("trt1", "ctl")
- PC
Integer, which principle component to use. Use to DefineBestPC if unsure.
- filter_thresh
Integer, a coverage threshold for filtering, where CpG coverage of all samples must be larger than this value.
Examples
ranks <- getPCRanks(eigen, IDs = c("trt", "ctl"), PC = 1)