removeComp {methylKit} | R Documentation

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

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

    ## S4 method for signature 'methylBaseDB'
    removeComp(mBase, comp, 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))

[Package methylKit version 1.12.0 Index]