R SDK for BaseSpace RESTful API
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Documentation for package ‘BaseSpaceR’ version 1.42.0
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A B C D F G H I L N O P R S T U misc
| BaseSpaceR-package | R SDK for BaseSpace RESTful API |
-- A --
| aAuth | Sample 'AppAuth' instance with 'browse global' scope |
| AppAuth | 'AppAuth' class |
| AppAuth-class | 'AppAuth' class |
| appResultCollection | 'AppResults' and '"AppResultsSummary"' objects |
| appResultCollection-class | 'AppResults' and '"AppResultsSummary"' objects |
| appResultItem | 'AppResults' and '"AppResultsSummary"' objects |
| appResultItem-class | 'AppResults' and '"AppResultsSummary"' objects |
| AppResults | 'AppResults' and '"AppResultsSummary"' objects |
| AppResults-class | 'AppResults' and '"AppResultsSummary"' objects |
| AppResults-method | 'AppResults' and '"AppResultsSummary"' objects |
| AppResultsSummary-class | 'AppResults' and '"AppResultsSummary"' objects |
| AppSessionAuth-class | 'AppSessionAuth' class |
| appSessionItem | 'AppSessions' object |
| appSessionItem-class | 'AppSessions' object |
| AppSessions | 'AppSessions' object |
| AppSessions-class | 'AppSessions' object |
| AppSessions-method | 'AppSessions' object |
| as.character-method | Internal methods |
| as.list-method | 'Item', 'Collection' and 'Response' objects |
| auth | 'Item', 'Collection' and 'Response' objects |
| auth-method | 'Item', 'Collection' and 'Response' objects |
| auth-method | Internal methods |
| authNativeClient | 'AppSessionAuth' class |
| authWebClient | 'AppSessionAuth' class |
-- B --
| BaseSpaceR | R SDK for BaseSpace RESTful API |
-- C --
| Collection-class | 'Item', 'Collection' and 'Response' objects |
| countAppResults | 'AppResults' and '"AppResultsSummary"' objects |
| countAppResults-method | 'AppResults' and '"AppResultsSummary"' objects |
| countAppSessions | 'AppSessions' object |
| countAppSessions-method | 'AppSessions' object |
| countFiles | 'Files' and 'FilesSummary' objects |
| countFiles-method | 'Files' and 'FilesSummary' objects |
| countGenomes | 'Genomes' and 'GenomesSummary' objects |
| countProjects | 'Projects' and 'ProjectsSummary' objects |
| countProjects-method | 'Projects' and 'ProjectsSummary' objects |
| countRuns | 'Runs' and 'RunsSummary' objects |
| countRuns-method | 'Runs' and 'RunsSummary' objects |
| countSamples | 'Samples' and 'SamplesSummary' objects |
| countSamples-method | 'Samples' and 'SamplesSummary' objects |
| createAppResults | 'AppResults' and '"AppResultsSummary"' objects |
| createAppResults-method | 'AppResults' and '"AppResultsSummary"' objects |
| createProject | 'Projects' and 'ProjectsSummary' objects |
| createProject-method | 'Projects' and 'ProjectsSummary' objects |
-- D --
| DateCreated | 'Item', 'Collection' and 'Response' objects |
| DateCreated-method | 'Item', 'Collection' and 'Response' objects |
| DisplayedCount | 'Item', 'Collection' and 'Response' objects |
| DisplayedCount-method | 'Item', 'Collection' and 'Response' objects |
-- F --
| fileCollection | 'Files' and 'FilesSummary' objects |
| fileCollection-class | 'Files' and 'FilesSummary' objects |
| fileItem | 'Files' and 'FilesSummary' objects |
| fileItem-class | 'Files' and 'FilesSummary' objects |
| Files | 'Files' and 'FilesSummary' objects |
| Files-class | 'Files' and 'FilesSummary' objects |
| Files-method | 'Files' and 'FilesSummary' objects |
| FilesSummary-class | 'Files' and 'FilesSummary' objects |
-- G --
| genomeCollection | 'Genomes' and 'GenomesSummary' objects |
| genomeCollection-class | 'Genomes' and 'GenomesSummary' objects |
| genomeItem | 'Genomes' and 'GenomesSummary' objects |
| genomeItem-class | 'Genomes' and 'GenomesSummary' objects |
| Genomes | 'Genomes' and 'GenomesSummary' objects |
| Genomes-class | 'Genomes' and 'GenomesSummary' objects |
| Genomes-method | 'Genomes' and 'GenomesSummary' objects |
| GenomesSummary-class | 'Genomes' and 'GenomesSummary' objects |
| getBAMs | High-level methods for 'Files' objects and related |
| getBAMs-method | High-level methods for 'Files' objects and related |
| getCoverage | Methods for accessing coverage data from BAM files |
| getCoverage-method | Methods for accessing coverage data from BAM files |
| getCoverageStats | Methods for accessing coverage data from BAM files |
| getCoverageStats-method | Methods for accessing coverage data from BAM files |
| getFiles | 'Files' and 'FilesSummary' objects |
| getFiles-method | 'Files' and 'FilesSummary' objects |
| getIndexedBam | High-level methods for 'Files' objects and related |
| getVariants | Methods for accessing varinant data |
| getVariants-method | Methods for accessing varinant data |
| getVariantSet | Methods for accessing varinant data |
| getVariantSet-method | Methods for accessing varinant data |
-- H --
| hasAccess | 'AppAuth' class |
| hasAccess-method | 'AppAuth' class |
| Href | 'Item', 'Collection' and 'Response' objects |
| Href-method | 'Item', 'Collection' and 'Response' objects |
| HrefBaseSpaceUI | 'Item', 'Collection' and 'Response' objects |
| HrefBaseSpaceUI-method | 'Item', 'Collection' and 'Response' objects |
-- I --
| Id | 'Item', 'Collection' and 'Response' objects |
| Id-method | 'Item', 'Collection' and 'Response' objects |
| initializeAuth | 'AppAuth' class |
| initializeAuth-method | 'AppAuth' class |
| Item-class | 'Item', 'Collection' and 'Response' objects |
| Items | 'Item', 'Collection' and 'Response' objects |
| Items-method | 'Item', 'Collection' and 'Response' objects |
-- L --
| length-method | 'Item', 'Collection' and 'Response' objects |
| Limit | 'Item', 'Collection' and 'Response' objects |
| Limit-method | 'Item', 'Collection' and 'Response' objects |
| listAppResults | 'AppResults' and '"AppResultsSummary"' objects |
| listAppResults-method | 'AppResults' and '"AppResultsSummary"' objects |
| listAppSessions | 'AppSessions' object |
| listAppSessions-method | 'AppSessions' object |
| listFiles | 'Files' and 'FilesSummary' objects |
| listFiles-method | 'Files' and 'FilesSummary' objects |
| listGenomes | 'Genomes' and 'GenomesSummary' objects |
| listGenomes-method | 'Genomes' and 'GenomesSummary' objects |
| listProjects | 'Projects' and 'ProjectsSummary' objects |
| listProjects-method | 'Projects' and 'ProjectsSummary' objects |
| listRuns | 'Runs' and 'RunsSummary' objects |
| listRuns-method | 'Runs' and 'RunsSummary' objects |
| listSamples | 'Samples' and 'SamplesSummary' objects |
| listSamples-method | 'Samples' and 'SamplesSummary' objects |
-- N --
| Name | 'Item', 'Collection' and 'Response' objects |
| Name-method | 'Item', 'Collection' and 'Response' objects |
-- O --
| Offset | 'Item', 'Collection' and 'Response' objects |
| Offset-method | 'Item', 'Collection' and 'Response' objects |
-- P --
| performOAuth | 'AppAuth' class |
| projectCollection | 'Projects' and 'ProjectsSummary' objects |
| projectCollection-class | 'Projects' and 'ProjectsSummary' objects |
| projectItem | 'Projects' and 'ProjectsSummary' objects |
| projectItem-class | 'Projects' and 'ProjectsSummary' objects |
| Projects | 'Projects' and 'ProjectsSummary' objects |
| Projects-class | 'Projects' and 'ProjectsSummary' objects |
| Projects-method | 'Projects' and 'ProjectsSummary' objects |
| ProjectsSummary-class | 'Projects' and 'ProjectsSummary' objects |
| putFiles | 'Files' and 'FilesSummary' objects |
| putFiles-method | 'Files' and 'FilesSummary' objects |
-- R --
| requestAccessToken | 'AppAuth' class |
| requestAccessToken-method | 'AppAuth' class |
| Response-class | 'Item', 'Collection' and 'Response' objects |
| ResponseStatus | Class '"ResponseStatus"' |
| ResponseStatus-class | Class '"ResponseStatus"' |
| runCollection | 'Runs' and 'RunsSummary' objects |
| runCollection-class | 'Runs' and 'RunsSummary' objects |
| runItem | 'Runs' and 'RunsSummary' objects |
| runItem-class | 'Runs' and 'RunsSummary' objects |
| Runs | 'Runs' and 'RunsSummary' objects |
| Runs-class | 'Runs' and 'RunsSummary' objects |
| Runs-method | 'Runs' and 'RunsSummary' objects |
| RunsSummary-class | 'Runs' and 'RunsSummary' objects |
-- S --
| sampleCollection | 'Samples' and 'SamplesSummary' objects |
| sampleCollection-class | 'Samples' and 'SamplesSummary' objects |
| sampleItem | 'Samples' and 'SamplesSummary' objects |
| sampleItem-class | 'Samples' and 'SamplesSummary' objects |
| Samples | 'Samples' and 'SamplesSummary' objects |
| Samples-class | 'Samples' and 'SamplesSummary' objects |
| Samples-method | 'Samples' and 'SamplesSummary' objects |
| SamplesSummary-class | 'Samples' and 'SamplesSummary' objects |
| ServiceURI | Class '"ServiceURI"' |
| ServiceURI-class | Class '"ServiceURI"' |
| show-method | Class '"ResponseStatus"' |
| show-method | 'Item', 'Collection' and 'Response' objects |
| show-method | Class '"ServiceURI"' |
| show-method | Internal methods |
| SortBy | 'Item', 'Collection' and 'Response' objects |
| SortBy-method | 'Item', 'Collection' and 'Response' objects |
| SortDir | 'Item', 'Collection' and 'Response' objects |
| SortDir-method | 'Item', 'Collection' and 'Response' objects |
| Status | 'Item', 'Collection' and 'Response' objects |
| Status-method | 'Item', 'Collection' and 'Response' objects |
-- T --
| TotalCount | 'Item', 'Collection' and 'Response' objects |
| TotalCount-method | 'Item', 'Collection' and 'Response' objects |
-- U --
| updateAppSessions | 'AppSessions' object |
| updateAppSessions-method | 'AppSessions' object |
| uri | Class '"ServiceURI"' |
| uri-method | Class '"ServiceURI"' |
| userItem | 'Users' objects and resources |
| userItem-class | 'Users' objects and resources |
| UserOwnedBy | 'Item', 'Collection' and 'Response' objects |
| UserOwnedBy-method | 'Item', 'Collection' and 'Response' objects |
| Users | 'Users' objects and resources |
| Users-class | 'Users' objects and resources |
| Users-method | 'Users' objects and resources |
-- misc --
| $-method | 'Item', 'Collection' and 'Response' objects |
| [-method | 'Item', 'Collection' and 'Response' objects |
| [[-method | 'Item', 'Collection' and 'Response' objects |