README.md

In HCAMatrixBrowser: Extract and manage matrix data from the Human Cell Atlas project

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

library(HCAMatrixBrowser)

hca <- HCAMatrix()

Quick Start

with bundle_fqids

my_fqids <-
    c("ffd3bc7b-8f3b-4f97-aa2a-78f9bac93775.2019-05-14T122736.345000Z",
    "f69b288c-fabc-4ac8-b50c-7abcae3731bc.2019-05-14T120110.781000Z")

loadHCAMatrix(hca, bundle_fqids = my_fqids)
#> class: LoomExperiment 
#> dim: 58347 2 
#> metadata(0):
#> assays(1): matrix
#> rownames: NULL
#> rowData names(9): Accession Gene ... genus_species isgene
#> colnames(2): 3c2180aa-0aa4-411f-98dc-73ef87b447ed 1cfe9423-21d1-4281-9f9d-3aaa07b8e1e8
#> colData names(38): CellID barcode ... specimen_from_organism.provenance.document_id total_umis
#> rowGraphs(0): NULL
#> colGraphs(0): NULL

with filter operations

hca1 <- filter(hca, bundle_uuid == "ffd3bc7b-8f3b-4f97-aa2a-78f9bac93775")
## filter print out
filters(hca1)
#> $op
#> [x] "="
#> 
#> $field
#> [1] "bundle_uuid"
#> 
#> $value
#> [1] "ffd3bc7b-8f3b-4f97-aa2a-78f9bac93775"

loadHCAMatrix(hca1)
#> class: LoomExperiment 
#> dim: 58347 1 
#> metadata(0):
#> assays(1): matrix
#> rownames: NULL
#> rowData names(9): Accession Gene ... genus_species isgene
#> colnames(1): 3c2180aa-0aa4-411f-98dc-73ef87b447ed
#> colData names(44): CellID analysis_protocol.protocol_core.protocol_id ... specimen_from_organism.provenance.document_id total_umis
#> rowGraphs(0): NULL
#> colGraphs(0): NULL

HCAMatrixBrowser documentation built on Nov. 8, 2020, 5:15 p.m.