MassArrayData-class {MassArray} | R Documentation |
A data structure containing MassArray data and associated information for a single amplicon
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, ...)
.
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
signature(x = "MassArrayData")
: ...
signature(x = "MassArrayData")
: ...
signature(x = "MassArrayData")
: ...
signature(.Object = "MassArrayData")
: ...
Reid F. Thompson (rthompso@aecom.yu.edu), John M. Greally (jgreally@aecom.yu.edu)
showClass("MassArrayData")