An S4 class for holding raw methylation data from an alignment pipeline.
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 genomic base/region.
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
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
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[ .
The following functions provides access to data slots of methylRaw:
methylRaw object can be coerced to
GRanges object via
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
# example of a raw methylation data 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")