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))

[Package PhIPData version 1.0.0 Index]