validationFunctions: ValidationFunctions

In Bioconductor/AnnotationHubData: Transform public data resources into Bioconductor Data Structures

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 [e-mail]

• 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 [e-mail] 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")

Bioconductor/AnnotationHubData documentation built on Oct. 31, 2024, 8:13 a.m.