methylKit (version 0.99.2)

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

# NOT RUN {
data(methylKit)

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

# }