validationFunctions {AnnotationHubData} | R Documentation |
Functions to assist in the validation process of creating the metadata.csv file for Hub Resources
getSpeciesList(verbose=FALSE) validSpecies(species, verbose=TRUE) suggestSpecies(query, verbose=FALSE, op=c("|", "&")) getValidSourceTypes() checkSpeciesTaxId(txid, species, verbose=TRUE) validDispatchClass(dc, verbose=TRUE)
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) |
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.
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
Lori Shepherd
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")