The segMeth class inherits from the
segClass class and contains data about potential
segments on the genome, together with counts for each of those segments.
Objects from the class
Objects can be created by calls of the form new("segMeth", ...,
seglens). However, more usually they will be created by calling the
processAD function.
Slots
coordinates:
A GRanges
object defining the coordinates of the segments.
replicates:
Object of class "factor". The
replicate structure for the samples.
locLikelihoods:
Object of class "DataFrame"
describing estimated likelihoods that each region defined in
‘coordinates’ is a locus in each replicate group.
Cs:
Object of class matrix. Contains the
number of methylated cytosines (which are sequenced as a ‘C’)
observed for each sample in each potential segment.
Ts:
Object of class matrix. Contains the
number of unmethylated cytosines (which are sequenced as a ‘T’)
observed for each sample in each potential segment.
nonconversion:
Object of class "numeric". The
(estimated) nonconversion rate (see Details) for each of the libraries.
Details
The @coordinates slot contains information on each of the potential
segments; specifically, chromosome, start and end of the segment,
together. Each row of the @coordinates slot should correspond to
the same row of the @C and @T slots.
The nonconversion slot is an estimate of the rate (for each library)
at which an unmethylated cytosine has failed to be converted by sodium
bisulphite treatment into thymine, and is thus recorded (incorrectly) as
methylated. In some cases, this can be estimated from considering
observed methylation rates on regions known to be unmethylated (e.g.,
chloroplasts) or by introducing unmethylated control sequences.
In almost all cases objects of this class should be produced by the
processAD function.
Methods
Methods 'new', 'dim', '[' and 'show' have been defined for this class.
Author(s)
Thomas J. Hardcastle
See Also
processAD, the function that will most often be used to
create objects of this class.
segClass, from which this class inherits.