Objects from the Class
Objects can be created by calls of the form new("MassArrayData", sequence, file, verbose, fwd.tag, rev.tag, fwd.primer, rev.primer, strand, lower.threshold, upper.threshold, header, skip, sep, comment.char, fill, method, position, ...).Slots
sequence:- Nucleotide sequence for unconverted amplicon
chr:- Chromosomal position of amplicon
start:- Chromosomal position of amplicon
end:- Chromosomal position of amplicon
strand:- DNA strand used for amplicon (can be '+' or '-')
fwd.tag:- Nucleotide tag sequence 5' of the forward primer
rev.tag:- T7-containing nucleotide tag sequence 5' of the reverse primer
fwd.primer:- Length (in bp) of forward primer
rev.primer:- Length (in bp) of reverse primer
lower.threshold:- Lower limit (in Da) of usable mass window (default: 1500)
upper.threshold:- Upper limit (in Da) of usable mass window (default: 7000)
fragments.T:- List containing objects of class
MassArrayFragment, corresponding to the T-cleavage reaction for the amplicon on the specified strand fragments.C:- List containing objects of class
MassArrayFragment, corresponding to the C-cleavage reaction for the amplicon on the specified strand samples:- List containing object of class
MassArraySpectrum, each corresponding to spectral data from a single sample groups:- List of the group name to which each sample belongs
CpG.data:- Matrix containing analyzed methylation data, where each row is a sample and each column is a CG dinucleotide site
CpG.data.combined:- Matrix containing methylation data combined from multiple objects (or collapsed from within a single object), where each row is a sample and each column is a CG dinucleotide site
Methods
- \$
signature(x = "MassArrayData"): ... - \$<-
signature(x = "MassArrayData"): ... - [
signature(x = "MassArrayData"): ... - initialize
signature(.Object = "MassArrayData"): ...