Package index • SigRepo

Connect to Database

newConnHandler(): newConnHandler
conn_init(): conn_init
init_handle(): init_handle
get_handle(): get_handle
clear_handle(): clear_handle

Search Data in Database

searchAssayType(): searchAssayType
searchCollection(): searchCollection
searchKeyword(): searchKeyword
searchOrganism(): searchOrganism
searchPhenotype(): searchPhenotype
searchPlatform(): searchPlatform
searchProteomicsFeatureSet(): searchProteomicsFeatureSet
searchSampleType(): searchSampleType
searchSignature(): searchSignature
searchTranscriptomicsFeatureSet(): searchTranscriptomicsFeatureSet
searchGeneticVariantsFeatureSet(): searchGeneticVariantsFeatureSet
searchMetabolomicsFeatureSet(): searchMetabolomicsFeatureSet
searchUser(): searchUser
searchGenesetEntry(): searchGenesetEntry
searchGenesetResource(): searchGenesetResource

Retrieve Data from Database

getAPIKey(): getAPIKey
getCollection(): getCollection
getSignature(): getSignature
getSignatureFeatureSet(): getSignatureFeatureSet

Import Data to Database

addCollection(): addCollection
addKeyword(): addKeyword
addOrganism(): addOrganism
addPhenotype(): addPhenotype
addPlatform(): addPlatform
addProteomicsFeatureSet(): addProteomicsFeatureSet
addProteomicsSignatureSet(): addProteomicsSignatureSet
addMetabolomicsFeatureSet(): addMetabolomicsFeatureSet
addMetabolomicsSignatureSet(): addMetabolomicsSignatureSet
addSampleType(): addSampleType
addSignature(): addSignature
addSignatureToCollection(): addSignatureToCollection
addTranscriptomicsFeatureSet(): addTranscriptomicsFeatureSet
addTranscriptomicsSignatureSet(): addTranscriptomicsSignatureSet
addUser(): addUser
addUserToSignature(): addUserToSignature
addUserToCollection(): addUserToCollection
addGenesetEntry(): addGenesetEntry
addGenesetResource(): addGenesetResource

Update Data in Database

updateCollectionMetadata(): updateCollectionMetadata
updateSignature(): updateSignature
updateUser(): updateUser
updateProteomicsFeatureSet(): updateProteomicsFeatureSet
updateTranscriptomicsFeatureSet(): updateTranscriptomicsFeatureSet

Delete Data from Database

deleteCollection(): deleteCollection
deleteOrganism(): deleteOrganism
deletePhenotype(): deletePhenotype
deletePlatform(): deletePlatform
deleteSampleType(): deleteSampleType
deleteSignature(): deleteSignature
deleteUser(): deleteUser
inActivateUser(): inActivateUser
removeSignatureFromCollection(): removeSignatureFromCollection

Compare Signatures

compareSignatures(): Compare signatures from the SigRepo database

Enrichment Analysis

prepareHypeRSignatures(): Build hypeR-ready signature vectors from SigRepo signatures
runHypeR(): Run hypeR enrichment directly from SigRepo signatures
runHyperGEM(): Run hypeR.GEM enrichment directly from SigRepo metabolomics signatures
hypergemAvailable(): Resolve whether hypeR.GEM is available
hypergemExport(): Retrieve an exported function from hypeR.GEM

Build Signature Objects

Construct and validate OmicSignature and OmicSignatureCollection objects before depositing them

createOmicSignature(): createOmicSignature
createOmicCollection(): createOmicCollection
createSignatureMetadata(): createSignatureMetadata
createCollectionMetadata(): createCollectionMetadata
checkOmicSignature(): checkOmicSignature
checkOmicCollection(): checkOmicCollection
protTransform(): protTransform

Controlled Vocabulary

The value sets SigRepo validates metadata against

signature_types: Exported signature types
assay_tbl: Exported assay table
metabolomics_feature_tables: metabolomics_feature_tables

Internal Helpers

Exported for use across the package and by the server, not part of the day-to-day interface. Listed so every help page is reachable.

addGeneticVariantsFeatureSet(): addGeneticVariantsFeatureSet
addGeneticVariantsSignatureSet(): addGeneticVariantsSignatureSet
addMetabolomicsNomenclature(): addMetabolomicsNomenclature
addSignatureWithID(): addSignatureWithID
build_api_url(): build_api_url
get_api_handle(): get_api_handle
stop_for_api_error(): stop_for_api_error
test_conn_handler: Exported connection handler
checkAssayType(): checkAssayType
checkDBTable(): checkDBTable
checkDuplicatedEmails(): checkDuplicatedEmails
checkPermissions(): checkPermissions
checkSignatureType(): checkSignatureType
checkTableInput(): checkTableInput
createHashKey(): createHashKey
getDBColNames(): getDBColNames
getNumOfObs(): getNumOfObs
getVariableID(): getVariableID
insert_table_sql(): insert_table_sql
lookup_table_sql(): lookup_table_sql
delete_table_sql(): delete_table_sql
print_messages(): print_messages
removeDuplicates(): removeDuplicates
resolveMetabolomicsFeatureConfig(): resolveMetabolomicsFeatureConfig
verbose(): verbose
showAssayTypeErrorMessage(): showAssayTypeErrorMessage
showGeneticVariantsErrorMessage(): showTranscriptomicsErrorMessage
showMetabolomicsAmbiguityMessage(): showMetabolomicsAmbiguityMessage
showMetabolomicsErrorMessage(): showMetabolomicsErrorMessage
showOrganismErrorMessage(): showOrganismErrorMessage
showPlatformErrorMessage(): showPlatformErrorMessage
showProteomicsErrorMessage(): showProteomicsErrorMessage
showSampleTypeErrorMessage(): showSampleTypeErrorMessage
showTranscriptomicsErrorMessage(): showTranscriptomicsErrorMessage

Example Data

Example signatures included in the package

LLFS_Aging_Gene_2023: Transcriptomic signature: Human aging (LLFS cohort, blood, 2023)
Myc_reduce_mice_liver_24m: Transcriptomic signature: Myc haploinsufficient mouse liver (Myc(+/-))
omic_signature_1: Transcriptomic signature: Myc haploinsufficient mouse liver (Myc(+/-))
omic_signature_2: Transcriptomic signature: Myc haploinsufficient mouse liver (Myc(+/-))
omic_signature_3: Transcriptomic signature: Myc haploinsufficient mouse liver (Myc(+/-), version 3)
omic_signature_4: Transcriptomic signature: Myc haploinsufficient mouse liver (Myc(+/-), version 4)