MEDME (version 1.32.0)

MEDMEset-class: Class "MEDMEset"

Description

This class is used in MEDME library to store MeDIP derived DNA-methylation estimates and to save further elaboration of these, in association with chromosomal and positional probe information

Objects from the Class

Objects can be created by calls of the form new("MEDMEset", ...). This object could initially host the MeDIP normalized logRatio data, as returned by the MEDME.readFiles function. Afterwards, the same obejct is returned by most of the MEDME library function. Each time, a new slot is filled with additional data, as smoothed logR or Absolute/Relative Methylation Scores (AMS and RMS respectively). At the end of the analysis, usually after a call to the MEDME.predict function, the MEDME.writeFiles function can be used to generate SGR or GFF files from this object.

Slots

chr:

Object of class "character" : the probe-level chromosome asignments

pos:

Object of class "numeric" : the probe-level genomic position

logR:

Object of class "matrix" : the probe-level un-trasformed normalized MeDIP logRatios for each sample

smoothed:

Object of class "matrix" : the probe-level smoothed MeDIP logRatios for each sample

AMS:

Object of class "matrix" : the probe-level Absolute Methylation Score for each sample

RMS:

Object of class "matrix" : the probe-level Relative Methylation Score for each sample

CGcounts:

Object of class "numeric" : the probe-level count of CpGs

organism:

Object of class "character" : the organism that the probe genomic positions are referring to, either hsa or mmu for homo sapiens or mus musculus respectively

Methods

[

signature(x = "MEDMEset"): subsets the object based on its probes and/or samples

AMS

signature(object = "MEDMEset"): extracts the Absolute Methylation Score from the AMS slot

CG

signature(object = "MEDMEset"): extracts the probe CpG count from the CGcounts slot

chr

signature(object = "MEDMEset"): extracts the probe chromosomal assignment

org

signature(object = "MEDMEset"): extracts the organism

initialize

signature(.Object = "MEDMEset"): automatically generates smoothed, AMS and RMS matrix when only the logR slot is filled

logR

signature(object = "MEDMEset"): extracts the matrix of MeDIP un-transformed logRatios

pos

signature(object = "MEDMEset"): extracts the probe genomic position

RMS

signature(object = "MEDMEset"): extracts the Relative Methylation Score from the RMS slot

show

signature(object = "MEDMEset"): prints a summary of the object content

smoothed

signature(object = "MEDMEset"): extracts the Absolute Methylation Score from the AMS slot

References

http://genome.cshlp.org/cgi/content/abstract/gr.080721.108v1

See Also

MEDME.readFiles, MEDME.writeFiles

Examples

showClass("MEDMEset")