dependency fix

Author: stemangiola

NAMESPACE

@@ -4,6 +4,7 @@ export(get_SingleCellExperiment)
 export(get_metadata)
 importFrom(BiocGenerics,cbind)
 importFrom(DBI,dbConnect)
+importFrom(HDF5Array,HDF5RealizationSink)
 importFrom(HDF5Array,loadHDF5SummarizedExperiment)
 importFrom(RSQLite,SQLITE_RO)
 importFrom(RSQLite,SQLite)

R/query.R

@@ -13,6 +13,8 @@
 #' @importFrom dplyr as_tibble
 #' @importFrom HDF5Array loadHDF5SummarizedExperiment
 #' @importFrom stringr str_remove
+#' @importFrom HDF5Array HDF5RealizationSink
+#' @importFrom HDF5Array loadHDF5SummarizedExperiment
 #'
 #' @export
 #'

README.md

@@ -14,13 +14,35 @@ library(tidySingleCellExperiment)
 Load the data
 
 ``` r
-hca_metadata = get_metadata()
+get_metadata()
 ```
 
+    ## # Source:   table<metadata> [?? x 48]
+    ## # Database: sqlite 3.39.2 [/vast/projects/RCP/human_cell_atlas/metadata.sqlite]
+    ##    .cell   .sample .samp…¹ assay assay…² cell_…³ cell_…⁴ devel…⁵ devel…⁶ disease
+    ##    <chr>   <chr>   <chr>   <chr> <chr>   <chr>   <chr>   <chr>   <chr>   <chr>  
+    ##  1 AAACCT… 5f20d7… D17PrP… 10x … EFO:00… basal … CL:000… 31-yea… HsapDv… normal 
+    ##  2 AAACCT… 5f20d7… D17PrP… 10x … EFO:00… basal … CL:000… 31-yea… HsapDv… normal 
+    ##  3 AAACCT… 5f20d7… D17PrP… 10x … EFO:00… lumina… CL:000… 31-yea… HsapDv… normal 
+    ##  4 AAACCT… 5f20d7… D17PrP… 10x … EFO:00… lumina… CL:000… 31-yea… HsapDv… normal 
+    ##  5 AAACCT… 5f20d7… D17PrP… 10x … EFO:00… basal … CL:000… 31-yea… HsapDv… normal 
+    ##  6 AAACCT… 5f20d7… D17PrP… 10x … EFO:00… basal … CL:000… 31-yea… HsapDv… normal 
+    ##  7 AAACCT… 5f20d7… D17PrP… 10x … EFO:00… basal … CL:000… 31-yea… HsapDv… normal 
+    ##  8 AAACGG… 5f20d7… D17PrP… 10x … EFO:00… basal … CL:000… 31-yea… HsapDv… normal 
+    ##  9 AAACGG… 5f20d7… D17PrP… 10x … EFO:00… lumina… CL:000… 31-yea… HsapDv… normal 
+    ## 10 AAACGG… 5f20d7… D17PrP… 10x … EFO:00… basal … CL:000… 31-yea… HsapDv… normal 
+    ## # … with more rows, 38 more variables: disease_ontology_term_id <chr>,
+    ## #   ethnicity <chr>, ethnicity_ontology_term_id <chr>, file_id <chr>,
+    ## #   is_primary_data.x <chr>, organism <chr>, organism_ontology_term_id <chr>,
+    ## #   sample_placeholder <chr>, sex <chr>, sex_ontology_term_id <chr>,
+    ## #   tissue <chr>, tissue_ontology_term_id <chr>, dataset_id <chr>,
+    ## #   collection_id <chr>, cell_count <int>, dataset_deployments <chr>,
+    ## #   is_primary_data.y <chr>, is_valid <int>, linked_genesets <int>, …
+
 Explore the HCA content
 
 ``` r
-hca_metadata |> 
+get_metadata() |> 
     distinct(tissue, file_id) |> 
     count(tissue) |> 
     arrange(desc(n))
@@ -48,33 +70,35 @@ Query
 ``` r
 options("restore_SingleCellExperiment_show" = TRUE)
 sce = 
-    hca_metadata |> 
+    get_metadata() |> 
     filter(
-        ethnicity == "African" & 
+         ethnicity == "African" & 
         assay %LIKE% "%10x%" & 
         tissue == "lung parenchyma" & 
         cell_type %LIKE% "%CD4%"
     ) |> 
+    
     get_SingleCellExperiment()
 ```
 
-    ## Reading 9 files.
+    ## Reading 1 files.
 
-    ## .........
+    ## .
 
 ``` r
 sce
 ```
 
     ## class: SingleCellExperiment 
-    ## dim: 60661 1571 
-    ## metadata(63): X_normalization batch_condition ... schema_version title
+    ## dim: 28024 1571 
+    ## metadata(0):
     ## assays(1): X
-    ## rownames(60661): TSPAN6 TNMD ... RP11-175I6.6 PRSS43P
+    ## rownames(28024): TSPAN6 TNMD ... RP11-107E5.4 RP11-299P2.2
     ## rowData names(0):
-    ## colnames(1571):
-    ##   ACAGCCGGTCCGTTAA_F02526_4fc10a6b85e5fa688b253db4e0db8ba0
-    ##   GGGAATGAGCCCAGCT_F02526_4fc10a6b85e5fa688b253db4e0db8ba0 ...
-    ##   TCGTAGAGTATATGGA_SC29_948efa032d715a169f9edae65c696836
-    ##   GACGTTACACTGTGTA_SC29_948efa032d715a169f9edae65c696836
-    ## colData names(45): .sample .sample_name ... created_at.y updated_at.y
+    ## colnames(1571): ACAGCCGGTCCGTTAA_F02526 GGGAATGAGCCCAGCT_F02526 ...
+    ##   TACAACGTCAGCATTG_SC84 CATTCGCTCAATACCG_F02526
+    ## colData names(47): .sample .sample_name ... file_id_db
+    ##   stringr..str_remove.stringr..str_remove..cell...sample...._...
+    ## reducedDimNames(0):
+    ## mainExpName: NULL
+    ## altExpNames(0):