IdConsensus: Create Consensus Sequences by Groups

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

Description

Forms a consensus sequence representing the sequences in each group.

Usage

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

Arguments

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.

Details

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.

Value

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.

Author(s)

Erik Wright DECIPHER@cae.wisc.edu

See Also

Seqs2DB

Examples

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


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