MEDMEset-class: Class "MEDMEset"
In MEDME: Modelling Experimental Data from MeDIP Enrichment

Description Objects from the Class Slots Methods Author(s) References See Also Examples

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 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.

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

[: 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