This object stores the raw mehylation data that is read
in through read function and extends
data.frame.The raw methylation data is basically
percent methylation values and read coverage values per
string for an identifier of the sample
string for genome assembly, ex: hg18,hg19,mm9
methylation context string, ex: CpG,CpH,CHH, etc.
resolution of methylation information, 'base' or 'region'
methylRaw class extends
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. Subsetting by
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[ .
The following functions provides access to data slots of
methylRaw object can be coerced to
GRanges object via
1 2 3 4 5 6 7 8 9 10 11 12 13 14
# example of a raw methylation data contained as a text file read.table(system.file("extdata", "control1.myCpG.txt", package = "methylKit"), header=TRUE,nrows=5) data(methylKit) # example of a methylRaw object head(methylRawList.obj[]) str(head(methylRawList.obj[])) library(GenomicRanges) #coercing methylRaw object to GRanges object my.gr=as(methylRawList.obj[],"GRanges")
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