percMethylation-methods: get percent methylation scores from methylBase or...

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

Description

get percent methylation scores from methylBase or methylBaseDB object

Usage

percMethylation(
  methylBase.obj,
  rowids = FALSE,
  save.txt = FALSE,
  chunk.size = 1e+06
)

## S4 method for signature 'methylBase'
percMethylation(methylBase.obj, rowids = FALSE)

## S4 method for signature 'methylBaseDB'
percMethylation(
  methylBase.obj,
  rowids = FALSE,
  save.txt = FALSE,
  chunk.size = 1e+06
)

Arguments

methylBase.obj	a methylBase or methylBaseDB object
rowids	if TRUE, matrix rownames have identifiers as base/region location (default:FALSE)
save.txt	if TRUE, the matrix will be written to a text file, but only for methylBaseDB objects (default: FALSE)
chunk.size	Number of rows to be taken as a chunk for processing the methylBaseDB objects (default: 1e6)

Value

matrix with percent methylation values per base/region across all samples, row names would be base/region identifiers

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.

Examples

data(methylKit)
mat=percMethylation(methylBase.obj)
head(mat)

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