stepB: Step B: Search and Download Sequences
In megaptera: MEGAPhylogeny Techniques in R
Description
Usage
Arguments
Details
Value
Note
Author(s)
References
See Also
Description
For any given project (see megapteraProj), this step searches the Nucleotide database on GenBank, downloads all sequences and stores them in a postgreSQL database table.
Usage
1
stepB(x)
Arguments
x
an object of class megapteraProj
Details
All accessions are stored under thier species name as appearing in the organism field at GenBank, information about infrageneric ranks is stripped of the taxon names before they are stored in the database.
Value
None. stepB is called for its side effects: (1) strings of DNA sequences with attribute data are stored in a pgSQL database; (2) a log file is written to the current working directory.
Note
The function is under development and the results should always be checked.
Author(s)
Christoph Heibl
References
http://www.ncbi.nlm.nih.gov/books/NBK25501/
See Also
megaptera documentation built on Jan. 15, 2017, 11:19 p.m.
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Description Usage Arguments Details Value Note Author(s) References See Also
Description
For any given project (see megapteraProj), this step searches the Nucleotide database on GenBank, downloads all sequences and stores them in a postgreSQL database table.
Usage
1 | stepB(x)
|
Arguments
x |
an object of class |
Details
All accessions are stored under thier species name as appearing in the organism field at GenBank, information about infrageneric ranks is stripped of the taxon names before they are stored in the database.
Value
None. stepB is called for its side effects: (1) strings of DNA sequences with attribute data are stored in a pgSQL database; (2) a log file is written to the current working directory.
Note
The function is under development and the results should always be checked.
Author(s)
Christoph Heibl
References
http://www.ncbi.nlm.nih.gov/books/NBK25501/
See Also
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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