clean_pkg: Cleans up illegal characters in packages generated by...
In khughitt/EuPathDB: Provides access to pathogen annotation resources available on EuPathDB databases
clean_pkg R Documentation
Cleans up illegal characters in packages generated by make_organismdbi(),
make_orgdb(), and make_txdb(). This attempts to fix some of the common
problems therein.
Description
The primary problem this function seeks to solve is derived from the fact
that some species names in the eupathdb contain characters which are not
allowed in orgdb/txdb/organismdbi instances. Thus this invokes a couple of
regular expressions in an attempt to make sure these generated packages are
actually installable.
Usage
clean_pkg(path, removal = "-like", replace = "", sqlite = TRUE)
Arguments
path
Location for the original Db/Dbi instance.
removal
String to remove from the instance.
replace
What to replace removal with, when necessary.
sqlite
Also modify the sqlite database?
Details
One thing I should consider is to add some of this logic to my eupath queries
rather than perform these clunky modifications to the already-generated
packages.
Value
A hopefully cleaner OrgDb/TxDb/OrganismDbi sqlite package.
khughitt/EuPathDB documentation built on Nov. 4, 2023, 4:19 a.m.
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.
| clean_pkg | R Documentation |
Cleans up illegal characters in packages generated by make_organismdbi(), make_orgdb(), and make_txdb(). This attempts to fix some of the common problems therein.
Description
The primary problem this function seeks to solve is derived from the fact that some species names in the eupathdb contain characters which are not allowed in orgdb/txdb/organismdbi instances. Thus this invokes a couple of regular expressions in an attempt to make sure these generated packages are actually installable.
Usage
clean_pkg(path, removal = "-like", replace = "", sqlite = TRUE)
Arguments
path |
Location for the original Db/Dbi instance. |
removal |
String to remove from the instance. |
replace |
What to replace removal with, when necessary. |
sqlite |
Also modify the sqlite database? |
Details
One thing I should consider is to add some of this logic to my eupath queries rather than perform these clunky modifications to the already-generated packages.
Value
A hopefully cleaner OrgDb/TxDb/OrganismDbi sqlite package.
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.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.