locusRef-class: Class "locusRef"
In heibl/megaptera: MEGAPhylogeny Techniques in R

Description Objects from the Class Slots Extends Author(s) See Also

Class for genetic input parameters for megapteraProj.

Objects can be created by calls of the form locusRef(..., not, search.fields = c("gene", "title"), reference.gi).

kind
sql: a vector of mode character holding a SQL-compatible transformation of the first alias for naming database tables.
aliases: a vector of mode character giving strings that should be seached for; the first element is taken to name the corresponding postgreSQL tables.
not: a vector of mode character giving strings that should be excluded from the search results; corresponds to the use of NOT in GenBank query.
search.fields: a vector of mode character setting the search fields (or attributes) of the Nucleotide database to be searched for the strings specified via the ... argument.
use.genomes: logical, if TRUE sequences of loci will be extracted from annotated genomes of chloroplasts and mitochondria. Due to the existance of different annotation styles, which might (still) be incompatible with megaptera, this option can be used to turn the extraction of sequences from whole genomes off.
align.method: a character string giving the alignment method in MAFFT. Available accuracy-oriented methods for less than 200 sequences are "localpair", "globalpair", and "genafpair"; "retree 1" and "retree 2" are for speed-oriented alignment. The default is "auto", which lets MAFFT choose an opproriate alignment method.
min.identity: numeric between 0 and 1, giving the minimum proportion of nucleotides required to be identical with the reference sequence in order to be included in an alignment (default: 0.75)
min.coverage: numeric between 0 and 1, giving the minimum proportion of nucleotide positions a sequence must have in common with the reference sequence in order to be included in an alignment (default: 0.5)
reference: a list of class DNAbin that contains reference sequences from GenBank.

Class "locus", directly.

Christoph Heibl

dbPars, taxon, and megapteraPars for defining of database parameters, taxa, and the pipeline's parameters, respectively, and megapteraProj for the bundling of input data.

heibl/megaptera documentation built on Jan. 17, 2021, 3:34 a.m.