docs/V1Api.md

In Bioconductor/hcamatrixapi: R Package Client for HCA Matrix Service

V1Api

All URIs are relative to https://$

Method | HTTP request | Description ------------- | ------------- | ------------- MatrixLambdasApiV1CoreGetFeatureDetail | GET /v1/features/{feature_name} | Get a information about a matrix feature type MatrixLambdasApiV1CoreGetFeatures | GET /v1/features | Get a list of available feature types MatrixLambdasApiV1CoreGetFieldDetail | GET /v1/fields/{field_name} | Get a description of a metadata field MatrixLambdasApiV1CoreGetFields | GET /v1/fields | Get a list of available metadata fields MatrixLambdasApiV1CoreGetFilterDetail | GET /v1/filters/{filter_name} | Get a description of a filter MatrixLambdasApiV1CoreGetFilters | GET /v1/filters | Get a list of permitted filters MatrixLambdasApiV1CoreGetFormatDetail | GET /v1/formats/{format_name} | Get a description of a matrix format MatrixLambdasApiV1CoreGetFormats | GET /v1/formats | Get a list of available matrix formats MatrixLambdasApiV1CoreGetMatrix | GET /v1/matrix/{request_id} | Get status and result of a matrix request MatrixLambdasApiV1CorePostMatrix | POST /v1/matrix | Request an expression matrix

MatrixLambdasApiV1CoreGetFeatureDetail

V1MatrixFeatureDetail MatrixLambdasApiV1CoreGetFeatureDetail(feature.name)

Get a information about a matrix feature type

Example

library(hcamatrixapi)

var.feature.name <- 'gene' # character | Feature type to describe

#Get a information about a matrix feature type
api.instance <- V1Api$new()
result <- api.instance$MatrixLambdasApiV1CoreGetFeatureDetail(var.feature.name)
dput(result)

Parameters

Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- feature.name | character| Feature type to describe | [default to 'gene']

Return type

V1MatrixFeatureDetail

Authorization

No authorization required

HTTP request headers

• Content-Type: Not defined
• Accept: application/json

HTTP response details

| Status code | Description | Response headers | |-------------|-------------|------------------| | 200 | Feature found. | - | | 404 | Feature not found. | - |

MatrixLambdasApiV1CoreGetFeatures

array[character] MatrixLambdasApiV1CoreGetFeatures()

Get a list of available feature types

Get a list of matrix feature types that a POST to /matrix will accept.

Example

library(hcamatrixapi)


#Get a list of available feature types
api.instance <- V1Api$new()
result <- api.instance$MatrixLambdasApiV1CoreGetFeatures()
dput(result)

Parameters

This endpoint does not need any parameter.

Return type

array[character]

Authorization

No authorization required

HTTP request headers

• Content-Type: Not defined
• Accept: application/json

HTTP response details

| Status code | Description | Response headers | |-------------|-------------|------------------| | 200 | Successfully return feature list. | - |

MatrixLambdasApiV1CoreGetFieldDetail

OneOfv1NumericFieldDetailv1CategoricalFieldDetail MatrixLambdasApiV1CoreGetFieldDetail(field.name)

Get a description of a metadata field

Get detailed information about an available metadata field.

Example

library(hcamatrixapi)

var.field.name <- 'field.name_example' # character | Field to describe.

#Get a description of a metadata field
api.instance <- V1Api$new()
result <- api.instance$MatrixLambdasApiV1CoreGetFieldDetail(var.field.name)
dput(result)

Parameters

Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- field.name | character| Field to describe. |

Return type

OneOfv1NumericFieldDetailv1CategoricalFieldDetail

Authorization

No authorization required

HTTP request headers

• Content-Type: Not defined
• Accept: application/json

HTTP response details

| Status code | Description | Response headers | |-------------|-------------|------------------| | 200 | Field found. | - | | 404 | Field not found. | - |

MatrixLambdasApiV1CoreGetFields

array[character] MatrixLambdasApiV1CoreGetFields()

Get a list of available metadata fields

Get a list of metadata field names that a POST to /matrix will accept.

Example

library(hcamatrixapi)


#Get a list of available metadata fields
api.instance <- V1Api$new()
result <- api.instance$MatrixLambdasApiV1CoreGetFields()
dput(result)

Parameters

This endpoint does not need any parameter.

Return type

array[character]

Authorization

No authorization required

HTTP request headers

• Content-Type: Not defined
• Accept: application/json

HTTP response details

| Status code | Description | Response headers | |-------------|-------------|------------------| | 200 | Successfully return field list. | - |

MatrixLambdasApiV1CoreGetFilterDetail

OneOfv1NumericFieldDetailv1CategoricalFieldDetail MatrixLambdasApiV1CoreGetFilterDetail(filter.name)

Get a description of a filter

Get detailed information about a filter that can be applied to the HCA expression data.

Example

library(hcamatrixapi)

var.filter.name <- 'filter.name_example' # character | Filter to describe.

#Get a description of a filter
api.instance <- V1Api$new()
result <- api.instance$MatrixLambdasApiV1CoreGetFilterDetail(var.filter.name)
dput(result)

Parameters

Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- filter.name | character| Filter to describe. |

Return type

OneOfv1NumericFieldDetailv1CategoricalFieldDetail

Authorization

No authorization required

HTTP request headers

• Content-Type: Not defined
• Accept: application/json

HTTP response details

| Status code | Description | Response headers | |-------------|-------------|------------------| | 200 | Filter found. | - | | 404 | Filter not found. | - |

MatrixLambdasApiV1CoreGetFilters

array[character] MatrixLambdasApiV1CoreGetFilters()

Get a list of permitted filters

Get a list of filters that a POST to /matrix will accept.

Example

library(hcamatrixapi)


#Get a list of permitted filters
api.instance <- V1Api$new()
result <- api.instance$MatrixLambdasApiV1CoreGetFilters()
dput(result)

Parameters

This endpoint does not need any parameter.

Return type

array[character]

Authorization

No authorization required

HTTP request headers

• Content-Type: Not defined
• Accept: application/json

HTTP response details

| Status code | Description | Response headers | |-------------|-------------|------------------| | 200 | Successfully return filter list. | - |

MatrixLambdasApiV1CoreGetFormatDetail

character MatrixLambdasApiV1CoreGetFormatDetail(format.name)

Get a description of a matrix format

Example

library(hcamatrixapi)

var.format.name <- 'loom' # character | Format to describe

#Get a description of a matrix format
api.instance <- V1Api$new()
result <- api.instance$MatrixLambdasApiV1CoreGetFormatDetail(var.format.name)
dput(result)

Parameters

Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- format.name | character| Format to describe | [default to 'loom']

Return type

character

Authorization

No authorization required

HTTP request headers

• Content-Type: Not defined
• Accept: application/json

HTTP response details

| Status code | Description | Response headers | |-------------|-------------|------------------| | 200 | Format found. | - | | 404 | Format not found. | - |

MatrixLambdasApiV1CoreGetFormats

array[character] MatrixLambdasApiV1CoreGetFormats()

Get a list of available matrix formats

Get a list of matrix formats that a POST to /matrix will accept.

Example

library(hcamatrixapi)


#Get a list of available matrix formats
api.instance <- V1Api$new()
result <- api.instance$MatrixLambdasApiV1CoreGetFormats()
dput(result)

Parameters

This endpoint does not need any parameter.

Return type

array[character]

Authorization

No authorization required

HTTP request headers

• Content-Type: Not defined
• Accept: application/json

HTTP response details

| Status code | Description | Response headers | |-------------|-------------|------------------| | 200 | Successfully return format list. | - |

MatrixLambdasApiV1CoreGetMatrix

V1MatrixGetResponse MatrixLambdasApiV1CoreGetMatrix(request.id)

Get status and result of a matrix request

Example

library(hcamatrixapi)

var.request.id <- 'request.id_example' # character | ID returned by a previous matrix request.

#Get status and result of a matrix request
api.instance <- V1Api$new()
result <- api.instance$MatrixLambdasApiV1CoreGetMatrix(var.request.id)
dput(result)

Parameters

Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- request.id | character| ID returned by a previous matrix request. |

Return type

V1MatrixGetResponse

Authorization

No authorization required

HTTP request headers

• Content-Type: Not defined
• Accept: application/json

HTTP response details

| Status code | Description | Response headers | |-------------|-------------|------------------| | 200 | Matrix request found. | - | | 404 | Matrix request id not found. | - |

MatrixLambdasApiV1CorePostMatrix

V1MatrixPostResponse MatrixLambdasApiV1CorePostMatrix(v1.matrix.request=var.v1.matrix.request)

Request an expression matrix

Request an expression matrix using a set of filters to be ANDed and applied to the HCA expression data.

Example

library(hcamatrixapi)

var.v1.matrix.request <- v1_MatrixRequest$new(v1_MatrixFilter$new(v1_LogicalFilterOperator$new(), "field_example", TODO), list("fields_example"), "format_example", "feature_example") # V1MatrixRequest | 

#Request an expression matrix
api.instance <- V1Api$new()
result <- api.instance$MatrixLambdasApiV1CorePostMatrix(v1.matrix.request=var.v1.matrix.request)
dput(result)

Parameters

Name | Type | Description | Notes ------------- | ------------- | ------------- | ------------- v1.matrix.request | V1MatrixRequest| | [optional]

Return type

V1MatrixPostResponse

Authorization

No authorization required

HTTP request headers

• Content-Type: application/json
• Accept: application/json

HTTP response details

| Status code | Description | Response headers | |-------------|-------------|------------------| | 202 | Matrix request accepted. | - | | 400 | Bad request. | - | | 413 | Filter entity too large. | - |

Bioconductor/hcamatrixapi documentation built on Nov. 6, 2019, 12:10 a.m.