Identifies sequences by a specific level of their taxonomic rank.
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A SQLite connection object or a character string specifying the path to the database file.
Character string specifying the table where the rank information is located.
Level of the taxonomic rank. (See details section below.)
Logical or a character string specifying the table name in which to add the result.
Logical indicating whether to print database queries and other information.
IdentifyByRank simply identifies a sequence by a specific level of its taxonomic rank. Requires that
rank information be present in the
tblName, such as that created by default when importing sequences from a GenBank formatted file.
The input parameter
level should be an integer giving the “level” of the taxonomic rank to choose as the identifier. Negative
levels are interpreted as being that many levels from the last level in each rank. The
level zero selects the base level (see below).
If the specified level of rank does not exist then the closest rank is chosen. Therefore, setting
Inf will always select the last taxonomic level (i.e., genus).
For example, a representative “rank” imported from a GenBank file is:
Eukaryota; Fungi; Ascomycota; Saccharomycotina; Saccharomycetes;
Saccharomycetales; Saccharomycetaceae; Saccharomyces.
0 would result in an
identifier of “Saccharomyces cerevisiae”, because it is on the first line. A
2 would return “Fungi”, and
-2 (second to last) would return “Saccharomycetaceae”. A
Inf would find the nearest level to the end, “Saccharomyces”.
data.frame with the
rank and corresponding identifier as
identifier. Note that quotes are stripped from identifiers to prevent problems that they may cause. The
origin gives the
rank preceding the
add2tbl is not
FALSE then the “identifier” column is updated in
Erik Wright DECIPHER@cae.wisc.edu
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