IdConsensus: Create Consensus Sequences by Groups

Description

Forms a consensus sequence representing the sequences in each group.

Usage

IdConsensus(dbFile, tblName = "DNA", identifier = "", type = "DNAStringSet", colName = "id", add2tbl = FALSE, 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 unambiguous abbreviation of) one of "DNAStringSet", "RNAStringSet", "AAStringSet", or "BStringSet".

colName

Column containing the group name of each sequence.

add2tbl

Logical or a character string specifying the table name in which to add the result.

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.

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.

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.

Examples

Run this code

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

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