zhang-ncbi/dataset_r_test
R Package Client for NCBI Datasets API

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docs/GeneApi.md

docs/GeneApi.md
In zhang-ncbi/dataset_r_test: R Package Client for NCBI Datasets API

GeneApi

All URIs are relative to https://api.ncbi.nlm.nih.gov/datasets/v1alpha

Method | HTTP request | Description ------------- | ------------- | ------------- DownloadGenePackage | GET /gene/id/{gene_ids}/download | Get a gene dataset by gene ID DownloadGenePackagePost | POST /gene/download | Get a gene dataset by POST GeneDownloadSummaryByAccession | GET /gene/accession/{accessions}/download_summary | Get gene download summary by RefSeq Accession GeneDownloadSummaryById | GET /gene/id/{gene_ids}/download_summary | Get gene download summary by GeneID GeneDownloadSummaryByPost | POST /gene/download_summary | Get gene download summary GeneDownloadSummaryByTaxAndSymbol | GET /gene/symbol/{symbols}/taxon/{taxon}/download_summary | Get gene download summary by gene symbol. GeneMetadataByAccession | GET /gene/accession/{accessions} | Get gene metadata by RefSeq Accession GeneMetadataById | GET /gene/id/{gene_ids} | Get gene metadata by GeneID GeneMetadataByPost | POST /gene | Get gene metadata GeneMetadataByTaxAndSymbol | GET /gene/symbol/{symbols}/taxon/{taxon} | Get gene metadata by gene symbol. GeneTaxNameQuery | GET /gene/taxon_suggest/{taxon_query} | Get a list of taxonomy names and IDs found in the gene dataset given a partial taxonomic name. GeneTaxTree | GET /gene/taxon/{taxon}/tree | Retrieve tax tree

DownloadGenePackage

data.frame DownloadGenePackage(gene.ids, include.annotation.type=var.include.annotation.type, sort.schema.field='SORT_FIELD_UNSPECIFIED', sort.schema.direction='SORT_DIRECTION_UNSPECIFIED', filename='ncbi_dataset.zip')

Get a gene dataset by gene ID

Get a gene dataset including gene, transcript and protein fasta sequence, annotation and metadata by gene ID.

Example

library(ncbi.datasets)

var.gene.ids <- list(123) # array[integer] | 
var.include.annotation.type <- list("include_annotation_type_example") # array[character] | Select additional types of annotation to include in the data package.  If unset, no annotation is provided.
var.sort.schema.field <- 'SORT_FIELD_UNSPECIFIED' # character | 
var.sort.schema.direction <- 'SORT_DIRECTION_UNSPECIFIED' # character | 
var.filename <- 'ncbi_dataset.zip' # character | Output file name.

#Get a gene dataset by gene ID
api.instance <- GeneApi$new()
result <- api.instance$DownloadGenePackage(var.gene.ids, include.annotation.type=var.include.annotation.type, sort.schema.field=var.sort.schema.field, sort.schema.direction=var.sort.schema.direction, filename=var.filename)
dput(result)

Parameters

Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- gene.ids | list( integer )| | include.annotation.type | Enum [FASTA_GENE, FASTA_RNA, FASTA_PROTEIN] | Select additional types of annotation to include in the data package. If unset, no annotation is provided. | [optional] sort.schema.field | Enum [SORT_FIELD_UNSPECIFIED, SORT_FIELD_GENE_ID, SORT_FIELD_GENE_TYPE, SORT_FIELD_GENE_SYMBOL] | | [optional] [default to 'SORT_FIELD_UNSPECIFIED'] sort.schema.direction | Enum [SORT_DIRECTION_UNSPECIFIED, SORT_DIRECTION_ASCENDING, SORT_DIRECTION_DESCENDING] | | [optional] [default to 'SORT_DIRECTION_UNSPECIFIED'] filename | character| Output file name. | [optional] [default to 'ncbi_dataset.zip']

Return type

data.frame

Authorization

No authorization required

HTTP request headers

HTTP response details

| Status code | Description | Response headers | |-------------|-------------|------------------| | 200 | Download selected gene data as a zip file. | - |

DownloadGenePackagePost

data.frame DownloadGenePackagePost(body, filename='ncbi_dataset.zip')

Get a gene dataset by POST

Get a gene dataset including gene, transcript and protein fasta sequence, annotation and metadata by POST.

Example

library(ncbi.datasets)

var.body <- v1alpha1GeneDatasetRequest$new(list("accessions_example"), list(123), list(GeneDatasetRequestFasta$new()), v1alpha1GeneDatasetRequestContentType$new(), GeneDatasetRequestSort$new(v1alpha1SortDirection$new(), GeneDatasetRequestSortField$new()), GeneDatasetRequestSymbolsForTaxon$new(list("symbols_example"), "taxon_example")) # V1alpha1GeneDatasetRequest | 
var.filename <- 'ncbi_dataset.zip' # character | Output file name.

#Get a gene dataset by POST
api.instance <- GeneApi$new()
result <- api.instance$DownloadGenePackagePost(var.body, filename=var.filename)
dput(result)

Parameters

Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- body | V1alpha1GeneDatasetRequest| | filename | character| Output file name. | [optional] [default to 'ncbi_dataset.zip']

Return type

data.frame

Authorization

No authorization required

HTTP request headers

HTTP response details

| Status code | Description | Response headers | |-------------|-------------|------------------| | 200 | Download selected gene data as a zip file. | - |

GeneDownloadSummaryByAccession

V1alpha1DownloadSummary GeneDownloadSummaryByAccession(accessions, returned.content='COMPLETE', sort.schema.field='SORT_FIELD_UNSPECIFIED', sort.schema.direction='SORT_DIRECTION_UNSPECIFIED')

Get gene download summary by RefSeq Accession

Get gene download summary by RefSeq Accession in a JSON output format.

Example

library(ncbi.datasets)

var.accessions <- list("inner_example") # array[character] | RNA or Protein accessions.
var.returned.content <- 'COMPLETE' # character | 
var.sort.schema.field <- 'SORT_FIELD_UNSPECIFIED' # character | 
var.sort.schema.direction <- 'SORT_DIRECTION_UNSPECIFIED' # character | 

#Get gene download summary by RefSeq Accession
api.instance <- GeneApi$new()
result <- api.instance$GeneDownloadSummaryByAccession(var.accessions, returned.content=var.returned.content, sort.schema.field=var.sort.schema.field, sort.schema.direction=var.sort.schema.direction)
dput(result)

Parameters

Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- accessions | list( character )| RNA or Protein accessions. | returned.content | Enum [COMPLETE, IDS_ONLY] | | [optional] [default to 'COMPLETE'] sort.schema.field | Enum [SORT_FIELD_UNSPECIFIED, SORT_FIELD_GENE_ID, SORT_FIELD_GENE_TYPE, SORT_FIELD_GENE_SYMBOL] | | [optional] [default to 'SORT_FIELD_UNSPECIFIED'] sort.schema.direction | Enum [SORT_DIRECTION_UNSPECIFIED, SORT_DIRECTION_ASCENDING, SORT_DIRECTION_DESCENDING] | | [optional] [default to 'SORT_DIRECTION_UNSPECIFIED']

Return type

V1alpha1DownloadSummary

Authorization

No authorization required

HTTP request headers

HTTP response details

| Status code | Description | Response headers | |-------------|-------------|------------------| | 200 | A successful response. | - | | 0 | An unexpected error response. | - |

GeneDownloadSummaryById

V1alpha1DownloadSummary GeneDownloadSummaryById(gene.ids, returned.content='COMPLETE', sort.schema.field='SORT_FIELD_UNSPECIFIED', sort.schema.direction='SORT_DIRECTION_UNSPECIFIED')

Get gene download summary by GeneID

Get a download summary by GeneID in a JSON output format.

Example

library(ncbi.datasets)

var.gene.ids <- list(123) # array[integer] | 
var.returned.content <- 'COMPLETE' # character | 
var.sort.schema.field <- 'SORT_FIELD_UNSPECIFIED' # character | 
var.sort.schema.direction <- 'SORT_DIRECTION_UNSPECIFIED' # character | 

#Get gene download summary by GeneID
api.instance <- GeneApi$new()
result <- api.instance$GeneDownloadSummaryById(var.gene.ids, returned.content=var.returned.content, sort.schema.field=var.sort.schema.field, sort.schema.direction=var.sort.schema.direction)
dput(result)

Parameters

Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- gene.ids | list( integer )| | returned.content | Enum [COMPLETE, IDS_ONLY] | | [optional] [default to 'COMPLETE'] sort.schema.field | Enum [SORT_FIELD_UNSPECIFIED, SORT_FIELD_GENE_ID, SORT_FIELD_GENE_TYPE, SORT_FIELD_GENE_SYMBOL] | | [optional] [default to 'SORT_FIELD_UNSPECIFIED'] sort.schema.direction | Enum [SORT_DIRECTION_UNSPECIFIED, SORT_DIRECTION_ASCENDING, SORT_DIRECTION_DESCENDING] | | [optional] [default to 'SORT_DIRECTION_UNSPECIFIED']

Return type

V1alpha1DownloadSummary

Authorization

No authorization required

HTTP request headers

HTTP response details

| Status code | Description | Response headers | |-------------|-------------|------------------| | 200 | A successful response. | - | | 0 | An unexpected error response. | - |

GeneDownloadSummaryByPost

V1alpha1DownloadSummary GeneDownloadSummaryByPost(body)

Get gene download summary

Get gene download summary in a JSON output format.

Example

library(ncbi.datasets)

var.body <- v1alpha1GeneDatasetRequest$new(list("accessions_example"), list(123), list(GeneDatasetRequestFasta$new()), v1alpha1GeneDatasetRequestContentType$new(), GeneDatasetRequestSort$new(v1alpha1SortDirection$new(), GeneDatasetRequestSortField$new()), GeneDatasetRequestSymbolsForTaxon$new(list("symbols_example"), "taxon_example")) # V1alpha1GeneDatasetRequest | 

#Get gene download summary
api.instance <- GeneApi$new()
result <- api.instance$GeneDownloadSummaryByPost(var.body)
dput(result)

Parameters

Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- body | V1alpha1GeneDatasetRequest| |

Return type

V1alpha1DownloadSummary

Authorization

No authorization required

HTTP request headers

HTTP response details

| Status code | Description | Response headers | |-------------|-------------|------------------| | 200 | A successful response. | - | | 0 | An unexpected error response. | - |

GeneDownloadSummaryByTaxAndSymbol

V1alpha1DownloadSummary GeneDownloadSummaryByTaxAndSymbol(symbols, taxon, returned.content='COMPLETE', sort.schema.field='SORT_FIELD_UNSPECIFIED', sort.schema.direction='SORT_DIRECTION_UNSPECIFIED')

Get gene download summary by gene symbol.

Get gene download summary by gene symbol in a JSON output format.

Example

library(ncbi.datasets)

var.symbols <- list("inner_example") # array[character] | 
var.taxon <- 'taxon_example' # character | 
var.returned.content <- 'COMPLETE' # character | 
var.sort.schema.field <- 'SORT_FIELD_UNSPECIFIED' # character | 
var.sort.schema.direction <- 'SORT_DIRECTION_UNSPECIFIED' # character | 

#Get gene download summary by gene symbol.
api.instance <- GeneApi$new()
result <- api.instance$GeneDownloadSummaryByTaxAndSymbol(var.symbols, var.taxon, returned.content=var.returned.content, sort.schema.field=var.sort.schema.field, sort.schema.direction=var.sort.schema.direction)
dput(result)

Parameters

Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- symbols | list( character )| | taxon | character| | returned.content | Enum [COMPLETE, IDS_ONLY] | | [optional] [default to 'COMPLETE'] sort.schema.field | Enum [SORT_FIELD_UNSPECIFIED, SORT_FIELD_GENE_ID, SORT_FIELD_GENE_TYPE, SORT_FIELD_GENE_SYMBOL] | | [optional] [default to 'SORT_FIELD_UNSPECIFIED'] sort.schema.direction | Enum [SORT_DIRECTION_UNSPECIFIED, SORT_DIRECTION_ASCENDING, SORT_DIRECTION_DESCENDING] | | [optional] [default to 'SORT_DIRECTION_UNSPECIFIED']

Return type

V1alpha1DownloadSummary

Authorization

No authorization required

HTTP request headers

HTTP response details

| Status code | Description | Response headers | |-------------|-------------|------------------| | 200 | A successful response. | - | | 0 | An unexpected error response. | - |

GeneMetadataByAccession

V1alpha1GeneMetadata GeneMetadataByAccession(accessions, returned.content='COMPLETE', sort.schema.field='SORT_FIELD_UNSPECIFIED', sort.schema.direction='SORT_DIRECTION_UNSPECIFIED')

Get gene metadata by RefSeq Accession

Get detailed gene metadata by RefSeq Accession in a JSON output format.

Example

library(ncbi.datasets)

var.accessions <- list("inner_example") # array[character] | RNA or Protein accessions.
var.returned.content <- 'COMPLETE' # character | 
var.sort.schema.field <- 'SORT_FIELD_UNSPECIFIED' # character | 
var.sort.schema.direction <- 'SORT_DIRECTION_UNSPECIFIED' # character | 

#Get gene metadata by RefSeq Accession
api.instance <- GeneApi$new()
result <- api.instance$GeneMetadataByAccession(var.accessions, returned.content=var.returned.content, sort.schema.field=var.sort.schema.field, sort.schema.direction=var.sort.schema.direction)
dput(result)

Parameters

Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- accessions | list( character )| RNA or Protein accessions. | returned.content | Enum [COMPLETE, IDS_ONLY] | | [optional] [default to 'COMPLETE'] sort.schema.field | Enum [SORT_FIELD_UNSPECIFIED, SORT_FIELD_GENE_ID, SORT_FIELD_GENE_TYPE, SORT_FIELD_GENE_SYMBOL] | | [optional] [default to 'SORT_FIELD_UNSPECIFIED'] sort.schema.direction | Enum [SORT_DIRECTION_UNSPECIFIED, SORT_DIRECTION_ASCENDING, SORT_DIRECTION_DESCENDING] | | [optional] [default to 'SORT_DIRECTION_UNSPECIFIED']

Return type

V1alpha1GeneMetadata

Authorization

No authorization required

HTTP request headers

HTTP response details

| Status code | Description | Response headers | |-------------|-------------|------------------| | 200 | A successful response. | - | | 0 | An unexpected error response. | - |

GeneMetadataById

V1alpha1GeneMetadata GeneMetadataById(gene.ids, returned.content='COMPLETE', sort.schema.field='SORT_FIELD_UNSPECIFIED', sort.schema.direction='SORT_DIRECTION_UNSPECIFIED')

Get gene metadata by GeneID

Get detailed gene metadata by GeneID in a JSON output format.

Example

library(ncbi.datasets)

var.gene.ids <- list(123) # array[integer] | 
var.returned.content <- 'COMPLETE' # character | 
var.sort.schema.field <- 'SORT_FIELD_UNSPECIFIED' # character | 
var.sort.schema.direction <- 'SORT_DIRECTION_UNSPECIFIED' # character | 

#Get gene metadata by GeneID
api.instance <- GeneApi$new()
result <- api.instance$GeneMetadataById(var.gene.ids, returned.content=var.returned.content, sort.schema.field=var.sort.schema.field, sort.schema.direction=var.sort.schema.direction)
dput(result)

Parameters

Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- gene.ids | list( integer )| | returned.content | Enum [COMPLETE, IDS_ONLY] | | [optional] [default to 'COMPLETE'] sort.schema.field | Enum [SORT_FIELD_UNSPECIFIED, SORT_FIELD_GENE_ID, SORT_FIELD_GENE_TYPE, SORT_FIELD_GENE_SYMBOL] | | [optional] [default to 'SORT_FIELD_UNSPECIFIED'] sort.schema.direction | Enum [SORT_DIRECTION_UNSPECIFIED, SORT_DIRECTION_ASCENDING, SORT_DIRECTION_DESCENDING] | | [optional] [default to 'SORT_DIRECTION_UNSPECIFIED']

Return type

V1alpha1GeneMetadata

Authorization

No authorization required

HTTP request headers

HTTP response details

| Status code | Description | Response headers | |-------------|-------------|------------------| | 200 | A successful response. | - | | 0 | An unexpected error response. | - |

GeneMetadataByPost

V1alpha1GeneMetadata GeneMetadataByPost(body)

Get gene metadata

Get detailed gene metadata in a JSON output format.

Example

library(ncbi.datasets)

var.body <- v1alpha1GeneDatasetRequest$new(list("accessions_example"), list(123), list(GeneDatasetRequestFasta$new()), v1alpha1GeneDatasetRequestContentType$new(), GeneDatasetRequestSort$new(v1alpha1SortDirection$new(), GeneDatasetRequestSortField$new()), GeneDatasetRequestSymbolsForTaxon$new(list("symbols_example"), "taxon_example")) # V1alpha1GeneDatasetRequest | 

#Get gene metadata
api.instance <- GeneApi$new()
result <- api.instance$GeneMetadataByPost(var.body)
dput(result)

Parameters

Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- body | V1alpha1GeneDatasetRequest| |

Return type

V1alpha1GeneMetadata

Authorization

No authorization required

HTTP request headers

HTTP response details

| Status code | Description | Response headers | |-------------|-------------|------------------| | 200 | A successful response. | - | | 0 | An unexpected error response. | - |

GeneMetadataByTaxAndSymbol

V1alpha1GeneMetadata GeneMetadataByTaxAndSymbol(symbols, taxon, returned.content='COMPLETE', sort.schema.field='SORT_FIELD_UNSPECIFIED', sort.schema.direction='SORT_DIRECTION_UNSPECIFIED')

Get gene metadata by gene symbol.

Get detailed gene metadata by gene symbol in a JSON output format.

Example

library(ncbi.datasets)

var.symbols <- list("inner_example") # array[character] | 
var.taxon <- 'taxon_example' # character | 
var.returned.content <- 'COMPLETE' # character | 
var.sort.schema.field <- 'SORT_FIELD_UNSPECIFIED' # character | 
var.sort.schema.direction <- 'SORT_DIRECTION_UNSPECIFIED' # character | 

#Get gene metadata by gene symbol.
api.instance <- GeneApi$new()
result <- api.instance$GeneMetadataByTaxAndSymbol(var.symbols, var.taxon, returned.content=var.returned.content, sort.schema.field=var.sort.schema.field, sort.schema.direction=var.sort.schema.direction)
dput(result)

Parameters

Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- symbols | list( character )| | taxon | character| | returned.content | Enum [COMPLETE, IDS_ONLY] | | [optional] [default to 'COMPLETE'] sort.schema.field | Enum [SORT_FIELD_UNSPECIFIED, SORT_FIELD_GENE_ID, SORT_FIELD_GENE_TYPE, SORT_FIELD_GENE_SYMBOL] | | [optional] [default to 'SORT_FIELD_UNSPECIFIED'] sort.schema.direction | Enum [SORT_DIRECTION_UNSPECIFIED, SORT_DIRECTION_ASCENDING, SORT_DIRECTION_DESCENDING] | | [optional] [default to 'SORT_DIRECTION_UNSPECIFIED']

Return type

V1alpha1GeneMetadata

Authorization

No authorization required

HTTP request headers

HTTP response details

| Status code | Description | Response headers | |-------------|-------------|------------------| | 200 | A successful response. | - | | 0 | An unexpected error response. | - |

GeneTaxNameQuery

V1alpha1SciNameAndIds GeneTaxNameQuery(taxon.query)

Get a list of taxonomy names and IDs found in the gene dataset given a partial taxonomic name.

This endpoint retrieves a list of taxonomy names and IDs found in the gene dataset given a partial taxonomic name of any rank.

Example

library(ncbi.datasets)

var.taxon.query <- 'taxon.query_example' # character | NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank

#Get a list of taxonomy names and IDs found in the gene dataset given a partial taxonomic name.
api.instance <- GeneApi$new()
result <- api.instance$GeneTaxNameQuery(var.taxon.query)
dput(result)

Parameters

Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- taxon.query | character| NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank |

Return type

V1alpha1SciNameAndIds

Authorization

No authorization required

HTTP request headers

HTTP response details

| Status code | Description | Response headers | |-------------|-------------|------------------| | 200 | A successful response. | - | | 0 | An unexpected error response. | - |

GeneTaxTree

V1alpha1Organism GeneTaxTree(taxon)

Retrieve tax tree

Example

library(ncbi.datasets)

var.taxon <- 'taxon_example' # character | NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank

#Retrieve tax tree
api.instance <- GeneApi$new()
result <- api.instance$GeneTaxTree(var.taxon)
dput(result)

Parameters

Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- taxon | character| NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank |

Return type

V1alpha1Organism

Authorization

No authorization required

HTTP request headers

HTTP response details

| Status code | Description | Response headers | |-------------|-------------|------------------| | 200 | A successful response. | - | | 0 | An unexpected error response. | - |



zhang-ncbi/dataset_r_test documentation built on Jan. 1, 2021, 1:52 p.m.

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