PrepareAnnotationGCF: Prepare an annotation set from an NCBI GCF assembly.
In chambm/customProDB: Generate customized protein databases from NGS data for proteomics search
Description
Usage
Arguments
Value
Author(s)
Examples
Description
Prepare an annotation set from an NCBI GCF assembly.
Usage
1
PrepareAnnotationGCF(ncbiFtpUrl, annotation_path, ...)
Arguments
ncbiFtpUrl
the location of _cds_from_genomic.fna, _translated_from_cds.faa, and _genomic.gff files
annotation_path
specify a folder to store all the annotations.
...
additional arguments
Value
No return value. It creates several .RData files in annotation_path containing annotations needed for further analysis.
Author(s)
Matt Chambers
Examples
1
2
annotation_path <- tempdir()
PrepareAnnotationGCF("ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/922/835/GCF_001922835.1_NIST_Tur_tru_v1/", annotation_path)
chambm/customProDB documentation built on May 31, 2019, 12:08 p.m.
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Description Usage Arguments Value Author(s) Examples
Description
Prepare an annotation set from an NCBI GCF assembly.
Usage
1 | PrepareAnnotationGCF(ncbiFtpUrl, annotation_path, ...)
|
Arguments
ncbiFtpUrl |
the location of _cds_from_genomic.fna, _translated_from_cds.faa, and _genomic.gff files |
annotation_path |
specify a folder to store all the annotations. |
... |
additional arguments |
Value
No return value. It creates several .RData files in annotation_path containing annotations needed for further analysis.
Author(s)
Matt Chambers
Examples
1 2 | annotation_path <- tempdir()
PrepareAnnotationGCF("ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/922/835/GCF_001922835.1_NIST_Tur_tru_v1/", annotation_path)
|
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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