SequenceData: An internal Reference Class to represent DNA data, read from...
In Ward9250/HybridCheck: Detection and dating of Recombinant Regions in DNA sequence data
Description
An internal Reference Class to represent DNA data, read from a FASTA file.
Fields
FullSequenceA DNAStringSet containing the full sequence alignment.
InformativeSequenceA DNAStringSet containing the elignment, with uninformative sites removed.
InformativeBpAn integer vector containing the base positions that are informative.
ReferenceSeqA character vector of length one with the sequence name that is the reference.
PopulationsA list of population definitions - a list of vectors containing sequence names.
Methods
InputDNA(intarget)Reads in sequences from file and appropriately modifies fields of the object.
enforceDNA()Enforces some rules about the content of the sequence object and throws errors should they occur.
getFullBp()Returns a vector containing the numbers of the base positions in the aligned sequences.
getFullLength()Returns the length in base pairs, of the aligned sequences.
getInformativeBp()Returns a vector of the base positions of the informative sites in the aligned sequences.
getInformativeLength()Returns the number in base pairs, of informative sites in the aligned sequences.
getSequenceNames()Returns a character vector of the sequence names.
hasDNA()Returns true if a DNA sequence alignment has been read in and stored in the object. Otherwise returns false.
hasPopulations()Returns TRUE when a set of populations has been defined. Otherwise returns FALSE.
htmlSummary()Creates a character vector of the summary of the sequence object, formatted as HTML.
initialize(sequenceInput = NULL)Initializes the object, may be provided with a filepath to a sequence file, currently only FASTA is supported.
namesOfPopulations()Returns the names of the populations.
numberOfPopulations()Returns the number of populations assigned.
numberOfSequences()Returns the number of sequences in the stored alignment.
oneSeqOnePop()Function assigns one population per sequence.
pullTriplet(selection)Extracts from the sequence object, a triplet of sequences.
setPopulations(pops)Define which sequences form a population. Provide a list of vectors containing either integers or sequence names.
textSummary()Creates a character vector of the summary of the sequence object.
Ward9250/HybridCheck documentation built on Jan. 30, 2022, 11:01 a.m.
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Description
An internal Reference Class to represent DNA data, read from a FASTA file.
Fields
FullSequenceA DNAStringSet containing the full sequence alignment.
InformativeSequenceA DNAStringSet containing the elignment, with uninformative sites removed.
InformativeBpAn integer vector containing the base positions that are informative.
ReferenceSeqA character vector of length one with the sequence name that is the reference.
PopulationsA list of population definitions - a list of vectors containing sequence names.
Methods
InputDNA(intarget)Reads in sequences from file and appropriately modifies fields of the object.
enforceDNA()Enforces some rules about the content of the sequence object and throws errors should they occur.
getFullBp()Returns a vector containing the numbers of the base positions in the aligned sequences.
getFullLength()Returns the length in base pairs, of the aligned sequences.
getInformativeBp()Returns a vector of the base positions of the informative sites in the aligned sequences.
getInformativeLength()Returns the number in base pairs, of informative sites in the aligned sequences.
getSequenceNames()Returns a character vector of the sequence names.
hasDNA()Returns true if a DNA sequence alignment has been read in and stored in the object. Otherwise returns false.
hasPopulations()Returns TRUE when a set of populations has been defined. Otherwise returns FALSE.
htmlSummary()Creates a character vector of the summary of the sequence object, formatted as HTML.
initialize(sequenceInput = NULL)Initializes the object, may be provided with a filepath to a sequence file, currently only FASTA is supported.
namesOfPopulations()Returns the names of the populations.
numberOfPopulations()Returns the number of populations assigned.
numberOfSequences()Returns the number of sequences in the stored alignment.
oneSeqOnePop()Function assigns one population per sequence.
pullTriplet(selection)Extracts from the sequence object, a triplet of sequences.
setPopulations(pops)Define which sequences form a population. Provide a list of vectors containing either integers or sequence names.
textSummary()Creates a character vector of the summary of the sequence object.
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