isValidKey {annotate} | R Documentation

## Get or verify valid IDs for a package or OrgDb object.

### Description

These functions either verify that a list of IDs are primary and valid IDs for a package, or else return all the valid primary IDs from a package

### Usage

    isValidKey(ids, pkg)
    allValidKeys(pkg)

    ## S4 method for signature 'character,character'
    isValidKey(ids, pkg)

    ## S4 method for signature 'character,OrgDb'
    isValidKey(ids, pkg)

    ## S4 method for signature 'character'
    allValidKeys(pkg)

    ## S4 method for signature 'OrgDb'
    allValidKeys(pkg)

### Arguments

`ids` | A character vector containing IDs that you wish to validate.
`pkg` | Either the name of an installed annotation package (e.g., "org.Hs.eg.db"), or an uninstalled annotation package, e.g., from AnnotationHub.

### Details

Every package has some kind of ID that is central to that package. For chip-based packages this will be some kind of probe, and for the organism based packages it will be something else (usually an entrez gene ID). isValidKey takes a list of IDs and tests to see whether or not they are present (valid) in a particular package. allValidKeys simply returns all the valid primary IDs for a package.

### Value

`isValidKey` returns a vector of TRUE or FALSE values corresponding to whether or not the ID is valid.

`allValidKeys` returns a vector of all the valid primary IDs.

### Author(s)

Marc Carlson

### See Also

`updateSymbolsToValidKeys`

### Examples

    ## Not run:
      ## 2 bad IDs and a 3rd that will be valid
      ids <- c("15S_rRNA_2","21S_rRNA_4","15S_rRNA")
      isValidKey(ids, "org.Sc.sgd")

      ## 2 good IDs and a 3rd that will not be valid
      ids <- c("5600","7531", "altSymbol")
      isValidKey(ids, "org.Hs.eg")

      ## Get all the valid primary id from org.Hs.eg.db
      allValidKeys("org.Hs.eg")

    ## End(Not run)

[Package annotate version 1.65.1 Index]