getSequenceByRegion: Read genome sequence data from user by inputing region
In quick2063706271/Cov2Comparator: Analyzing SARS covid-2 genome across different geographic regions
Description
Usage
Arguments
Value
References
Examples
Description
A function that takes region as input. It will look up the accessionID of
SARS-COV2 of this region. Then it will retrieve the sequence from NCBI
database online and return as a DNAStringSet object.
Usage
1
getSequenceByRegion(region)
Arguments
region
A string indicating the interested region in which SARS-COV2
are located that you want to study
Value
Returns a DNAStringSet with sequences.
References
H. Pagès, P. Aboyoun, R. Gentleman and S. DebRoy (2020). Biostrings:
Efficient manipulation of biological strings.
R package version 2.58.0. https://bioconductor.org/packages/Biostrings
Paradis E. & Schliep K. (2019). ape 5.0: an environment for modern
phylogenetics and evolutionary
analyses in R. Bioinformatics 35: 526-528.
Examples
1
2
3
4
5
# Example 1
# Load MT066156.1 (accessionID of SARS-COV2 in Italy) by
# using "Italy" as input
region <- "Italy"
italySequence <- getSequenceByRegion(region)
quick2063706271/Cov2Comparator documentation built on Dec. 22, 2021, 10:59 a.m.
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Description Usage Arguments Value References Examples
Description
A function that takes region as input. It will look up the accessionID of SARS-COV2 of this region. Then it will retrieve the sequence from NCBI database online and return as a DNAStringSet object.
Usage
1 | getSequenceByRegion(region)
|
Arguments
region |
A string indicating the interested region in which SARS-COV2 are located that you want to study |
Value
Returns a DNAStringSet with sequences.
References
H. Pagès, P. Aboyoun, R. Gentleman and S. DebRoy (2020). Biostrings: Efficient manipulation of biological strings. R package version 2.58.0. https://bioconductor.org/packages/Biostrings
Paradis E. & Schliep K. (2019). ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R. Bioinformatics 35: 526-528.
Examples
1 2 3 4 5 | # Example 1
# Load MT066156.1 (accessionID of SARS-COV2 in Italy) by
# using "Italy" as input
region <- "Italy"
italySequence <- getSequenceByRegion(region)
|
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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