aliases {PhIPData}

R Documentation

Using aliases to subset virus data

Description

Rather than typing out full viruses names or repeating regexpressions, users can use aliases as a convenient tool to subset PhIPData objects by viral species.

Usage

getAliasPath()

setAliasPath(path)

getAlias(virus)

setAlias(virus, pattern)

deleteAlias(virus)

Arguments

path	path to alias.rda
virus	character vector of the alias
pattern	character vector of regexpressions corresponding to the alias

Details

Aliases are saved to an rda file containing only a data.frame with two columns: alias and pattern. The alias column contains the alias while the pattern column contains the corresponding regexpression of interest.

The location of the alias database is returned and defined by getAliasPath and setAliasPath, respectively. By default getAliasPath points to the extdata package folder.

Once an alias is added to the database, it can always be accessed once the package is loaded. It is recommended to use the functions setAlias and deleteAlias to edit the alias database rather than modify the .rda file itself. If an alias already exists in the database, setAlias replaces the matched pattern. If an alias does not exist in the database, getAlias returns NA_character_.

Value

getAliasPath() returns the path to the alias database. getAlias() returns a vector of regexpressions corresponding to queried inputs. The returned vector is the same length as the input vector. Queries that do not exist in the database return NA_character_.

Functions

• getAliasPath: return the path to the .rda file of aliases.

• setAliasPath: set the path to the .rda file of aliases.

• getAlias: return a regexpression corresponding to the alias.

• setAlias: define/modify the regexpression for an alias.

• deleteAlias: remove an alias from the database.

Examples

## Get and set path to alias.rda
getAliasPath()
## Not run: 
setAliasPath("examplepath/alias.rda")

## End(Not run)

## Edit and modify aliases in the database
setAlias("test_virus", "test_pattern")
getAlias("test_virus")
setAlias("test_virus", "test_pattern2")
getAlias("test_virus")
deleteAlias("test_virus")

## Edit and modify multiple aliases at once.
setAlias(c("virus_1", "virus_2"), c("pattern_1", "pattern_2"))
getAlias(c("virus_1", "virus_2"))
deleteAlias(c("virus_1", "virus_2"))

## Example of how to subset HIV using `getAlias`
## Often, it is useful to set the `ignore.case` of `grep`/`grepl` to TRUE.
counts_dat <- matrix(1:10, nrow = 5)
peptide_meta <- data.frame(species = c(
    rep("Epstein-Barr virus", 2),
    rep("human immunodeficiency virus", 3)
))

phip_obj <- PhIPData(counts = counts_dat, peptideInfo = peptide_meta)
subset(phip_obj, grepl(getAlias("HIV"), species, ignore.case = TRUE))

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