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项目作者： Bioconductor

项目描述 ：
:warning: DEPRECATED :warning: Download Matrix Data using the HCA API
高级语言： R
项目地址: git://github.com/Bioconductor/HCAMatrixBrowser.git
创建时间： 2018-11-21T18:37:12Z
项目社区：https://github.com/Bioconductor/HCAMatrixBrowser
开源协议：
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" class="reference-link">HCAMatrixBrowser

Overview

HCAMatrixBrowser gives users access to the matrix download service for
the Human Cell Atlas project.

It provides a main function for downloading data matrices from either a
set of bundle_fqids or a data filters.

  • loadHCAMatrix allows either a vector of bundle_fqids or an added
    filter operation to the HCA API object

API object

  1. library(HCAMatrixBrowser)
  2. #> Loading required package: AnVIL
  3. #> Loading required package: dplyr
  4. #> 
  5. #> Attaching package: 'dplyr'
  6. #> The following objects are masked from 'package:stats':
  7. #> 
  8. #>     filter, lag
  9. #> The following objects are masked from 'package:base':
  10. #> 
  11. #>     intersect, setdiff, setequal, union
  12. #> 
  13. #> Attaching package: 'HCAMatrixBrowser'
  14. #> The following object is masked from 'package:dplyr':
  15. #> 
  16. #>     filter
  17. #> The following object is masked from 'package:stats':
  18. #> 
  19. #>     filter
  21. hca <- HCAMatrix()

Quick Start

with bundle_fqids

  1. my_fqids <-
  2.     c("ffd3bc7b-8f3b-4f97-aa2a-78f9bac93775.2019-05-14T122736.345000Z",
  3.     "f69b288c-fabc-4ac8-b50c-7abcae3731bc.2019-05-14T120110.781000Z")
  5. loadHCAMatrix(hca, bundle_fqids = my_fqids)
  6. #> class: LoomExperiment 
  7. #> dim: 58347 2 
  8. #> metadata(0):
  9. #> assays(1): matrix
  10. #> rownames: NULL
  11. #> rowData names(9): Accession Gene ... genus_species isgene
  12. #> colnames(2): 3c2180aa-0aa4-411f-98dc-73ef87b447ed
  13. #>   1cfe9423-21d1-4281-9f9d-3aaa07b8e1e8
  14. #> colData names(38): CellID barcode ...
  15. #>   specimen_from_organism.provenance.document_id total_umis
  16. #> rowGraphs(0): NULL
  17. #> colGraphs(0): NULL

with filter operations

  1. hca1 <- filter(hca, bundle_uuid == "ffd3bc7b-8f3b-4f97-aa2a-78f9bac93775")
  2. ## filter print out
  3. filters(hca1)
  4. #> $op
  5. #> [x] "="
  6. #> 
  7. #> $field
  8. #> [x] "bundle_uuid"
  9. #> 
  10. #> $value
  11. #> [x] "ffd3bc7b-8f3b-4f97-aa2a-78f9bac93775"
  13. loadHCAMatrix(hca1)
  14. #> class: LoomExperiment 
  15. #> dim: 58347 1 
  16. #> metadata(0):
  17. #> assays(1): matrix
  18. #> rownames: NULL
  19. #> rowData names(9): Accession Gene ... genus_species isgene
  20. #> colnames(1): 3c2180aa-0aa4-411f-98dc-73ef87b447ed
  21. #> colData names(44): CellID analysis_protocol.protocol_core.protocol_id
  22. #>   ... specimen_from_organism.provenance.document_id total_umis
  23. #> rowGraphs(0): NULL
  24. #> colGraphs(0): NULL