reconstruct-methods: Reconstruct methylBase object based on a new methylation...

In vd4mmind/methylkit: DNA methylation analysis from high-throughput bisulfite sequencing results

Description

The function reconstructs a new methylBase object from an input methylBase object and percent methylation matrix. Basically, it uses the read coverages in the input methylBase object and deduces new number of methylated Cs and unmethylated Cs based on the input percent methylation matrix. It is ideally to be used to reconstruct methylBase objects after batch correction on percent methylation values. The percent methylation matrix rows must match methylBase object rows in order ,and in addition column order (the order of samples) in input methylBase must match the order in percent methylation matrix.

Usage

  reconstruct(methMat, mBase)

Arguments

methMat	percent methylation matrix, row order and order of the samples same as the methylBase object
mBase	methylBase object to be reconstructed

Value

new methylBase object where methylation percentage matches input methMat and coverages matches input mBase

Note

Batch effect correction (if any batch effect exists) is a tricky issue. We provide some simple ways to deal with it (see assocComp and removeComp ), But if you can find other ways to correct for batch effects and want to create a methylBase object with the corrected percent methylation values, you can use this function.

Author(s)

Altuna Akalin

Examples

data(methylKit)

# get percent methylation
mat=percMethylation(methylBase.obj)

# do some changes in the matrix
# this is just a toy example
# ideally you want to correct the matrix
# for batch effects
mat[mat==100]=80

# reconstruct the methylBase from the corrected matrix
newobj=reconstruct(mat,methylBase.obj)

vd4mmind/methylkit documentation built on May 3, 2019, 4:57 p.m.