getCoverageStats-methods: get coverage stats from methylRaw object

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

get coverage stats from methylRaw object

Description

The function returns basic statistics about read coverage per base. It can also plot a histogram of read coverage values.

Usage

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

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

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

Arguments

object	a methylRaw or methylRawDB object
plot	plot a histogram of coverage if TRUE (default:FALSE)
both.strands	do stats and plot for both strands if TRUE (default: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 coverage 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 coverage stats for the first sample in methylRawList.obj object
getCoverageStats(methylRawList.obj[[1]],plot=TRUE,
both.strands=FALSE,labels=TRUE)

al2na/methylKit documentation built on Nov. 30, 2024, 5:44 p.m.