IdConsensus: Create Consensus Sequences by Groups
In DECIPHER: Tools for curating, analyzing, and manipulating biological sequences

Description Usage Arguments Details Value Author(s) See Also Examples

Forms a consensus sequence representing the sequences in each group.

IdConsensus(dbFile,
            tblName = "Seqs",
            identifier = "",
            type = "DNAStringSet",
            colName = "identifier",
            processors = 1,
            verbose = TRUE,
            ...)

`dbFile`	A SQLite connection object or a character string specifying the path to the database file.
`tblName`	Character string specifying the table in which to form consensus.
`identifier`	Optional character string used to narrow the search results to those matching a specific identifier. If "" then all identifiers are selected.
`type`	The type of `XStringSet` (sequences) to use in forming consensus. This should be (an abbreviation of) one of `"DNAStringSet"`, `"RNAStringSet"`, `"AAStringSet"`, or `"BStringSet"`.
`colName`	Column containing the group name of each sequence.
`processors`	The number of processors to use, or `NULL` to automatically detect and use all available processors.
`verbose`	Logical indicating whether to display progress.
`...`	Additional arguments to be passed directly to `ConsensusSequence` for an `AAStringSet`, `DNAStringSet`, or `RNAStringSet`, or to `consensusString` for a `BStringSet`.

Creates a consensus sequence for each of the distinct groups defined in colName. The resulting XStringSet contains as many consensus sequences as there are distinct groups in colName. For example, it is possible to create a set of consensus sequences with one consensus sequence for each "id" in the tblName.

An XStringSet object containing the consensus sequence for each group. The names of the XStringSet contain the number of sequences and name of each group.

Erik Wright eswright@pitt.edu

Seqs2DB

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db <- system.file("extdata", "Bacteria_175seqs.sqlite", package="DECIPHER")
con <- IdConsensus(db, colName="identifier", noConsensusChar="N")
BrowseSeqs(con)