ncbiNucleotide: NCBI Nucleotide database
In cstubben/genomes2: Genome sequencing project metadata
Description
Usage
Arguments
Details
Value
Author(s)
References
See Also
Examples
Description
Search Entrez Nucleotide at NCBI and retrieve summary tables
Usage
1
ncbiNucleotide(term)
Arguments
term
Any valid combination of Entrez search terms or a vector of accessions numbers
Details
Returns a summary from Entrez Nucleotide.
Value
A genomes data frame with acc, name, released, taxid, size, gi and other fields
Author(s)
Chris Stubben
References
A description of the Entrez programming utilities is at
http://eutils.ncbi.nlm.nih.gov/.
See Also
Examples
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## Not run:
ncbiNucleotide("AL117189,AL109969,AL117211")[,1:6]
# Exclude Patents and Refseq
marb <- ncbiNucleotide( "Marburgvirus[ORGN] NOT gbdiv_pat[PROP] NOT srcdb_refseq[PROP]")
head(marb)
# two peaks in size distribution (partial and complete sequences)
hist(marb$size, col="blue", br=30, main="Marburg virus sequences", xlab="Length (bp)")
## End(Not run)
cstubben/genomes2 documentation built on May 14, 2019, 12:25 p.m.
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Description Usage Arguments Details Value Author(s) References See Also Examples
Description
Search Entrez Nucleotide at NCBI and retrieve summary tables
Usage
1 | ncbiNucleotide(term)
|
Arguments
term |
Any valid combination of Entrez search terms or a vector of accessions numbers |
Details
Returns a summary from Entrez Nucleotide.
Value
A genomes data frame with acc, name, released, taxid, size, gi and other fields
Author(s)
Chris Stubben
References
A description of the Entrez programming utilities is at http://eutils.ncbi.nlm.nih.gov/.
See Also
Examples
1 2 3 4 5 6 7 8 9 10 | ## Not run:
ncbiNucleotide("AL117189,AL109969,AL117211")[,1:6]
# Exclude Patents and Refseq
marb <- ncbiNucleotide( "Marburgvirus[ORGN] NOT gbdiv_pat[PROP] NOT srcdb_refseq[PROP]")
head(marb)
# two peaks in size distribution (partial and complete sequences)
hist(marb$size, col="blue", br=30, main="Marburg virus sequences", xlab="Length (bp)")
## End(Not run)
|
R Package Documentation
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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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