Objects from the Class
Objects can be created by calls of the form new("MassArrayFragment", ID, sequence, assay.name, name, position, type, direction, extra, bisulfite.converted, assayable, primer, ...).Slots
ID:- Unique integer indexing the fragment's position within a potential list of multiple fragments
assay.name:- (currently not supported)
name:- (currently not supported)
sequence:- Bisulphite converted nucleotide sequence of fragment
position:- Relative position of fragment within the amplicon
length:- Length (in bp) of fragment sequence
CpGs:- Number of CG dinucleotides contained within the fragment
MW:- Predicted molecular weight(s) of fragment, including methylated and unmethylated mass, adducts, etc.
collisions:- Number of fragments that share the same molecular weight as the current fragment
collision.IDs:- IDs of other fragments that share the same molecular weight as the current fragment
CG.collisions:- Number of CG-containing fragments that share the same molecular weight as the current fragment
CG.collision.IDs:- IDs of other CG-containing fragments that share the same molecular weight as the current fragment
type:- Specifies either 'T' or 'C' cleavage reaction
direction:- DNA strand used for fragment sequence (can be '+' or '-')
extra:- One of "5PPP-3P", "5OH", or "5PPP-3OH" (default)
bisulfite.converted:- Logical indicating whether the fragment sequence represents bisulfite converted sequence
assayable:- Logical indicating whether or not the fragment molecular weight is within the usable mass window
conversion.control:- Logical indicating whether or not the fragment is designated as a potential conversion control
required:- Logical indicating whether or not the fragment is designated as 'required' by the user
ignored:- Logical indicating whether or not the fragment is to be ignored
primer:- Logical indicating whether or not the fragment overlaps with primer or tagged sequence
Methods
- \$
signature(x = "MassArrayFragment"): ... - \$<-
signature(x = "MassArrayFragment"): ... - initialize
signature(.Object = "MassArrayFragment"): ...