## ----eval=FALSE--------------------------------------------------------------- # if (!requireNamespace("BiocManager", quietly = TRUE) # install.packages("BiocManager") # # BiocManager::install("HCABrowser") # BiocManager::install("HCAMatrixBrowser") ## ----include=TRUE,results="hide",message=FALSE,warning=FALSE------------------ library(HCABrowser) library(HCAMatrixBrowser) ## ----eval=FALSE--------------------------------------------------------------- # hcabrowser <- HCABrowser::HCABrowser() # # res <- hcabrowser %>% filter( # library_construction_approach.ontology == "EFO:0008931" & # paired_end == True & # specimen_from_organism_json.biomaterial_core.ncbi_taxon_id == 9606 # ) # # (bundle_fqids <- res %>% pullBundles) ## ----------------------------------------------------------------------------- bundle_fqids <- c("ffd3bc7b-8f3b-4f97-aa2a-78f9bac93775.2019-05-14T122736.345000Z", "f69b288c-fabc-4ac8-b50c-7abcae3731bc.2019-05-14T120110.781000Z", "f8ba80a9-71b1-4c15-bcfc-c05a50660898.2019-05-14T122536.545000Z", "fd202a54-7085-406d-a92a-aad6dd2d3ef0.2019-05-14T121656.910000Z", "fffe55c1-18ed-401b-aa9a-6f64d0b93fec.2019-05-17T233932.932000Z") ## ----------------------------------------------------------------------------- hca <- HCAMatrix() ## ----------------------------------------------------------------------------- (lex <- loadHCAMatrix(hca, bundle_fqids = bundle_fqids, format = "loom")) ## ----------------------------------------------------------------------------- head(colnames(lex)) ## ----------------------------------------------------------------------------- hca1 <- filter(hca, bundle_uuid == "ffd3bc7b-8f3b-4f97-aa2a-78f9bac93775") ## ----------------------------------------------------------------------------- filters(hca1) ## ----------------------------------------------------------------------------- loadHCAMatrix(hca1, format = "loom") ## ----------------------------------------------------------------------------- hca2 <- filter(hca, dss_bundle_fqid %in% bundle_fqids) ## ----------------------------------------------------------------------------- filters(hca2) ## ----------------------------------------------------------------------------- loadHCAMatrix(hca2)