tileMethylCounts-methods: Get methylated/unmethylated base counts for tilling windows

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

Description

The function summarizes methylated/unmethylated base counts over tilling windows accross genome. This function can be used when differential methylation analysis is preferable to tilling windows instead of base pairs.

Usage

tileMethylCounts(object,win.size=1000,step.size=1000,cov.bases=0,mc.cores=1,save.db,...)

## S4 method for signature 'methylRaw'
tileMethylCounts(
  object,
  win.size = 1000,
  step.size = 1000,
  cov.bases = 0,
  mc.cores = 1,
  save.db = FALSE,
  ...
)

## S4 method for signature 'methylRawList'
tileMethylCounts(
  object,
  win.size = 1000,
  step.size = 1000,
  cov.bases = 0,
  mc.cores = 1,
  save.db = FALSE,
  ...
)

## S4 method for signature 'methylBase'
tileMethylCounts(
  object,
  win.size = 1000,
  step.size = 1000,
  cov.bases = 0,
  mc.cores = 1,
  save.db = FALSE,
  ...
)

## S4 method for signature 'methylRawDB'
tileMethylCounts(
  object,
  win.size = 1000,
  step.size = 1000,
  cov.bases = 0,
  mc.cores = 1,
  save.db = TRUE,
  ...
)

## S4 method for signature 'methylRawListDB'
tileMethylCounts(
  object,
  win.size = 1000,
  step.size = 1000,
  cov.bases = 0,
  mc.cores = 1,
  save.db = TRUE,
  ...
)

## S4 method for signature 'methylBaseDB'
tileMethylCounts(
  object,
  win.size = 1000,
  step.size = 1000,
  cov.bases = 0,
  mc.cores = 1,
  save.db = TRUE,
  ...
)

Arguments

object	methylRaw, methylRawDB, methylRawList, methylRawListDB, methylBase or methylBaseDB object containing base pair resolution methylation information
win.size	an integer for the size of the tiling windows
step.size	an integer for the step size of tiling windows
cov.bases	minimum number of bases to be covered in a given window
mc.cores	number of cores to use when processing methylDB objects, default: 1, but always 1 for Windows)
save.db	A Logical to decide whether the resulting object should be saved as flat file database or not, default: explained in Details sections
...	optional Arguments used when save.db is TRUE suffix A character string to append to the name of the output flat file database, only used if save.db is true, default actions: append “_tiled” to current filename if database already exists or generate new file with filename “sampleID_tiled” or “methylBase_tiled” dependent on input object dbdir The directory where flat file database(s) should be stored, defaults to getwd(), working directory for newly stored databases and to same directory for already existing database

Value

methylRaw,methylBase or methylRawList object

Details

The parameter chunk.size is only used when working with methylRawDB, methylBaseDB 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.

The parameter save.db is per default TRUE for methylDB objects as methylRawDB, methylBaseDB or methylRawListDB, while being per default FALSE for methylRaw, methylBase or methylRawList. If you wish to save the result of an in-memory-calculation as flat file database or if the size of the database allows the calculation in-memory, then you might want to change the value of this parameter.

Examples

data(methylKit)

tiled.methylRaw=tileMethylCounts(object=methylRawList.obj,win.size=1000,
                                 step.size=1000,cov.bases=0)

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