DECIPHER (version 2.0.2)

ConsensusSequence: Create a Consensus Sequence

Description

Forms a consensus sequence representing a set of sequences.

Usage

ConsensusSequence(myXStringSet, threshold = 0.05, ambiguity = TRUE, noConsensusChar = "+", minInformation = 0.75, ignoreNonBases = FALSE, includeTerminalGaps = FALSE)

Arguments

myXStringSet

An AAStringSet, DNAStringSet, or RNAStringSet object of aligned sequences.

threshold

Numeric giving the maximum fraction of sequence information that can be lost in the consensus sequence.

ambiguity

Logical specifying whether to consider ambiguity as split between their respective nucleotides. Degeneracy codes are specified in the IUPAC_CODE_MAP.

noConsensusChar

Single character from the sequence's alphabet giving the base to use when there is no consensus in a position.

minInformation

Minimum fraction of information required to form consensus in each position.

ignoreNonBases

Logical specifying whether to count gap ("-"), mask ("+"), and unknown (".") characters towards the consensus.

includeTerminalGaps

Logical specifying whether or not to include terminal gaps ("-" or "." characters on each end of the sequence) into the formation of consensus.

Value

An XStringSet with a single consensus sequence matching the input type.

Details

Two key parameters control the degree of consensus: threshold and minInformation. The default threshold (0.05) means that at most 5% of sequences will not be represented by the consensus sequence at any given position. The default minInformation (0.75) specifies that at least 75% of sequences must contain the information in the consensus, otherwise the noConsensusChar is used. If the specified threshold results in the choice of an ambiguity code that does not represent minInformation fraction of the sequences, then the noConsensusChar is used.

If ambiguity = TRUE (the default) then degeneracy codes are split between their respective bases according to the IUPAC_CODE_MAP for DNA/RNA, or AMINO_ACID_CODE for AA. For example, an ``R'' in a DNAStringSet would count as half an ``A'' and half a ``G''. If ambiguity = FALSE then degeneracy codes are not considered in forming the consensus. For an AAStringSet input, the lack of degeneracy codes generally results in ``X'' in positions with mismatches, unless the threshold is set higher than 0.05 (the default).

If includeNonBases = TRUE (the default) then gap ("-"), mask ("+"), and unknown (".") characters are counted towards the consensus, otherwise they are omitted from calculation of the consensus. Note that gap ("-") and unknown (".") characters are treated interchangeably as gaps when forming the consensus sequence. For this reason, the consensus of a position with all unknown (".") characters will be a gap ("-"). Also, note that if consensus is formed between different length sequences then it will represent only the longest sequences at the end. For this reason the consensus sequence is generally based on a sequence alignment so that all of the sequences will have equal lengths.

See Also

Disambiguate, IdConsensus, Seqs2DB

Examples

dna <- DNAStringSet(c("ANGCT-","-ACCT-"))
ConsensusSequence(dna)
# returns "ANSCT-"

aa <- AAStringSet(c("ANQIH-", "ADELW."))
ConsensusSequence(aa)
# returns "ABZJX-"

AAAT <- DNAStringSet(c("A", "A", "A", "T"))
ConsensusSequence(AAAT) # "W"
ConsensusSequence(AAAT, threshold=0.3) # "A"
ConsensusSequence(AAAT, threshold=0.3, minInformation=0.8) # "+"
ConsensusSequence(AAAT, threshold=0.3, minInformation=0.8, noConsensusChar="N") # "N"