getMethylationStats-methods: get Methylation stats from methylRaw or methylRawDB object

In al2na/methylKit: DNA methylation analysis from high-throughput bisulfite sequencing results

get Methylation stats from methylRaw or methylRawDB object

Description

The function returns basic statistics about It can also plot a histogram of

Usage

getMethylationStats(
  object,
  plot = FALSE,
  both.strands = FALSE,
  labels = TRUE,
  ...,
  chunk.size = 1e+06
)

## S4 method for signature 'methylRaw'
getMethylationStats(
  object,
  plot = FALSE,
  both.strands = FALSE,
  labels = TRUE,
  ...,
  chunk.size = 1e+06
)

## S4 method for signature 'methylRawDB'
getMethylationStats(
  object,
  plot = FALSE,
  both.strands = FALSE,
  labels = TRUE,
  ...,
  chunk.size = 1e+06
)

Arguments

object	a methylRaw or methylRawDB object
plot	plot a histogram of Methylation if TRUE (deafult:FALSE)
both.strands	do plots and stats for both strands seperately if TRUE (deafult:FALSE)
labels	should the bars of the histrogram have labels showing the percentage of values in each bin (default:TRUE)
...	options to be passed to hist function.
chunk.size	Number of rows to be taken as a chunk for processing the methylRawDB objects (default: 1e6)

Value

a summary of Methylation statistics or plot a histogram of coverage

Details

The parameter chunk.size is only used when working with methylRawDB or methylRawListDB 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)

# gets Methylation stats for the first sample in methylRawList.obj object
getMethylationStats(methylRawList.obj[[1]],plot=TRUE,
both.strands=FALSE,labels=TRUE)

al2na/methylKit documentation built on Feb. 1, 2024, 4:42 p.m.