isValidkey: Get or verify valid IDs for a package or OrgDb object.

In annotate: Annotation for microarrays

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)

annotate documentation built on Nov. 8, 2020, 8:14 p.m.