removeComp-methods: Remove principal components from a methylBase object

In methylKit: DNA methylation analysis from high-throughput bisulfite sequencing results

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, chunk.size = 1e+06, save.db = FALSE, ...)

## S4 method for signature 'methylBase'
removeComp(mBase, comp = NULL, chunk.size = 1e+06, save.db = FALSE, ...)

## S4 method for signature 'methylBaseDB'
removeComp(mBase, comp = NULL, chunk.size = 1e+06, save.db = TRUE, ...)

Arguments

mBase	methylBase or methylBaseDB object with no NA values, that means all bases should be covered in all samples.
comp	vector of component numbers to be removed
chunk.size	Number of rows to be taken as a chunk for processing the methylBaseDB objects (default: 1e6)
save.db	A Logical to decide whether the resulting object should be saved as flat file database or not, default: explained in Details sections
...	optional Arguments used when save.db is TRUE suffix A character string to append to the name of the output flat file database, only used if save.db is true, default actions: append “_reconstructed” to current filename if database already exists or generate new file with filename “methylBase_reconstructed” dbdir The directory where flat file database(s) should be stored, defaults to getwd(), working directory for newly stored databases and to same directory for already existing database dbtype The type of the flat file database, currently only option "tabix"

Value

new methylBase or methylBaseDB object

Details

The parameter chunk.size is only used when working with methylBaseDB objects, as they are read in chunk by chunk to enable processing large-sized objects which are stored as flat file database. Per default the chunk.size is set to 1M rows, which should work for most systems. If you encounter memory problems or have a high amount of memory available feel free to adjust the chunk.size.

The parameter save.db is per default TRUE for methylDB objects as methylBaseDB, while being per default FALSE for methylBase. If you wish to save the result of an in-memory-calculation as flat file database or if the size of the database allows the calculation in-memory, then you might want to change the value of this parameter.

Examples

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))

methylKit documentation built on Jan. 30, 2021, 2 a.m.