getMethylDiff-methods: get differentially methylated regions/bases based on cutoffs

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

Description

The function subsets a methylDiff or methylDiffDB object in order to get differentially methylated bases/regions satisfying thresholds.

Usage

getMethylDiff(
  .Object,
  difference = 25,
  qvalue = 0.01,
  type = "all",
  chunk.size = 1e+06,
  save.db = FALSE,
  ...
)

## S4 method for signature 'methylDiff'
getMethylDiff(
  .Object,
  difference = 25,
  qvalue = 0.01,
  type = "all",
  chunk.size = 1e+06,
  save.db = FALSE,
  ...
)

## S4 method for signature 'methylDiffDB'
getMethylDiff(
  .Object,
  difference = 25,
  qvalue = 0.01,
  type = "all",
  chunk.size = 1e+06,
  save.db = TRUE,
  ...
)

Arguments

.Object	a methylDiff or methylDiffDB object
difference	cutoff for absolute value of methylation percentage change between test and control (default:25)
qvalue	cutoff for qvalue of differential methylation statistic (default:0.01)
type	one of the "hyper","hypo" or "all" strings. Specifies what type of differentially menthylated bases/regions should be returned. For retrieving Hyper-methylated regions/bases type="hyper", for hypo-methylated type="hypo" (default:"all")
chunk.size	Number of rows to be taken as a chunk for processing the methylDiffDB objects (default: 1e6)
save.db	A Logical to decide whether the resulting object should be saved as flat file database or not, default: see Details
...	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 “_type” to current filename if database already exists or generate new file with filename “methylDiff_type” 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 dbtype The type of the flat file database, currently only option is "tabix" (only used for newly stored databases)

Value

a methylDiff or methylDiffDB object containing the differential methylated locations satisfying the criteria

Details

The parameter chunk.size is only used when working with methylDiffDB 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 methylDiffDB, while being per default FALSE for methylDiff. 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)

# get differentially methylated bases/regions with specific cutoffs
all.diff=getMethylDiff(methylDiff.obj,difference=25,qvalue=0.01,type="all")

# get hyper-methylated
hyper=getMethylDiff(methylDiff.obj,difference=25,qvalue=0.01,type="hyper")

# get hypo-methylated
hypo=getMethylDiff(methylDiff.obj,difference=25,qvalue=0.01,type="hypo")

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