Description Slots Details Subsetting Coercion Accessors Examples
This class is designed to hold statistics and locations for differentially
methylated regions/bases. It extends data.frame
class.
calculateDiffMeth
function returns an object
with methylDiff
class.
sample.ids
ids/names of samples in a vector
assembly
a name of genome assembly, such as :hg18,mm9, etc
context
numeric vector identifying which samples are which group
treatment
numeric vector identifying which samples are which group
destranded
logical denoting if methylation inormation is destranded or not
resolution
string either 'base' or 'region' defining the resolution of methylation information
.Data
data.frame holding the locations and statistics
methylDiff
class extends data.frame
class therefore
providing novice and experienced R users with a data structure that is
well known and ubiquitous in many R packages.
In the following code snippets, x
is a methylDiff
object.
Subsetting by x[i,]
will produce a new object if subsetting is done
on rows. Column subsetting is not directly allowed to prevent errors in the
downstream analysis. see ?methylKit[ .
methylDiff
object can be coerced to
GRanges
object via as
function.
The following functions provides access to data slots of methylDiffDB:
- getData
: get the data slot from the methylKit objects,
- getAssembly
: get assembly of the genome,
- getContext
: get the context of methylation
1 2 3 | data(methylKit)
library(GenomicRanges)
my.gr=as(methylDiff.obj,"GRanges")
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.