validationFunctions {AnnotationHubData} | R Documentation

## ValidationFunctions

### Description

Functions to assist in the validation process of creating the metadata.csv file for Hub Resources

### Usage

    getSpeciesList(verbose=FALSE)

    validSpecies(species, verbose=TRUE)

    suggestSpecies(query, verbose=FALSE, op=c("|", "&"))

    getValidSourceTypes()

    checkSpeciesTaxId(txid, species, verbose=TRUE)

    validDispatchClass(dc, verbose=TRUE)

### Arguments

`species` | species to validate (may be single value or list)
`query` | terms to query. Whether AND or OR is determined by argument op.
`verbose` | should additional information and useful tips be displayed
`op` | Should searching of mulitple terms be conditional OR ("|") or AND ("&")
`txid` | taxonomy id (single value or list)
`dc` | Dispatch class to validate (may be single value or list)

### Details

- getSpeciesList: Provides a list of valid species as determined by the GenomeInfoDbData package specData.rda file.

- validSpecies: True/False if argument is considered a valid species based on the list generated by getSpeciesList. A species may be deemed invalid if the capitalization mismatches or punctuation mismatches. Use suggestSpecies to find similar terms.

- suggestSpecies: Based on a term or multiple terms suggest possible valid species.

- getValidSourceTypes: returns list of acceptable values for SourceType in metadata.csv. If you think a valid source type should be added to the list please reach out to maintainer@bioconductor.org

- checkSpeciesTaxId: cross validates a list of species and taxonomy ids for expected values based on `GenomeInfoDb::loadTaxonomyDb()`. Warning when there is a mismatch.

- validDispatchClass: TRUE/FALSE if argument is considered a valid DispatchClass based on the currently available methods in AnnotationHub. Use `AnnotationHub::DispatchClassList()` to see the table of currently available methods. If a currently available method is not appropriate for your resource, please reach out to Lori Shepherd Lori.Shepherd@roswellpark.org to request a new method be added.

### Value

- For getSpeciesList: character vector of valid species

- For validSpecies: True/False if all species given as argument are valid

- For suggestSpecies: data.frame of taxonomy id and species name of possible valid species based on given query key words.

- For getValidSourceTypes: character vector of valid source types.

- For checkSpeciesTaxId: NULL if check is verfified, If verbose is ture a table of suggested values along with the warning.

- For validDispatchClass: True/False if all dispatch class given as argument are valid

### Author(s)

Lori Shepherd

### See Also

- AnnotationHubMetadata

- makeAnnotationHubMetadata

### Examples

    species = getSpeciesList()

    # following is TRUE

    validSpecies("Homo sapiens")
    # followin is FALSE because of starting "h"
    validSpecies("homo sapiens")

    # can provide multiple, if any are not valid FALSE
    # TRUE
    validSpecies(c("Homo sapiens", "Canis domesticus"))

    suggestSpecies("Canis")

    getValidSourceTypes()

    checkSpeciesTaxId(1003232, "Edhazardia aedis")
    checkSpeciesTaxId(9606, "Homo sapiens")

    validDispatchClass("GRanges")

[Package AnnotationHubData version 1.20.2 Index]