methylKit (version 0.9.5)

removeComp: Remove principal components from a methylBase object

Description

This function can remove a given principal componet from a given methylBase object. First, it calculates principal components from percent methylation matrix and removes the given component(s), reconstructs the methylation matrix then reconstructs number of methylated and unmethylated Cs per position based on the reconstructed percent methylation matrix, and finally returns a new methylBase object.

Usage

removeComp(mBase, comp = NULL)

Arguments

mBase

methylBase object with no NA values, that means all bases should be covered in all samples.

comp

vector of component numbers to be removed

Value

new methylBase object

Examples

# NOT RUN {
data(methylKit)

# remove 1st principal component
newObj=removeComp(methylBase.obj,comp=1)

# remove 3rd and 4th  principal components
newObj=removeComp(methylBase.obj,comp=c(3,4))
# }