ReciprocalBestBlast: A generic reciprocal best blast search.
In npcooley/Heron: A Package of Various Genomics Tools
Description
Usage
Arguments
Examples
View source: R/ReciprocalBestBlast.R
Description
Perform reciprocal best BLAST searches on set of genomes and their associated genomes specified by GenomeIDs. Uses an e-value cutoff of 1e-6, and the smith-waterman traceback options. BLAST must be installed locally and accessible by R.
Usage
1
ReciprocalBestBlast(PATH, ListOfGeneCalls, GenomeIDs, Align.Fast = FALSE)
Arguments
PATH
A character vector specifying the location of a sqlite database built by DECIPHER.
ListOfGeneCalls
A named list of data.frames, one for each genome in SyntenyObject, with named columns "Index", "Start", "Stop", "Strand", and an optional "Annotation" column.
GenomeIDs
A vector of characters specifying the identifiers to select from the database specified by PATH, and the list locations to select from in ListOfGeneCalls.
Align.Fast
Logical, run semi-redundant DECIPHER alignment of paired sequences.
Examples
1
npcooley/Heron documentation built on April 4, 2020, 10:24 p.m.
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Description Usage Arguments Examples
View source: R/ReciprocalBestBlast.R
Description
Perform reciprocal best BLAST searches on set of genomes and their associated genomes specified by GenomeIDs. Uses an e-value cutoff of 1e-6, and the smith-waterman traceback options. BLAST must be installed locally and accessible by R.
Usage
1 | ReciprocalBestBlast(PATH, ListOfGeneCalls, GenomeIDs, Align.Fast = FALSE)
|
Arguments
PATH |
A character vector specifying the location of a sqlite database built by DECIPHER. |
ListOfGeneCalls |
A named list of data.frames, one for each genome in SyntenyObject, with named columns "Index", "Start", "Stop", "Strand", and an optional "Annotation" column. |
GenomeIDs |
A vector of characters specifying the identifiers to select from the database specified by PATH, and the list locations to select from in ListOfGeneCalls. |
Align.Fast |
Logical, run semi-redundant DECIPHER alignment of paired sequences. |
Examples
1 |
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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