## ---- include = FALSE--------------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE ) ## ----install, eval = FALSE---------------------------------------------------- # ## install from Bioconductor if you haven't already # pkgs <- c("LoomExperiment", "hca") # pkgs_needed <- pkgs[!pkgs %in% rownames(installed.packages())] # BiocManager::install(pkgs_needed) ## ----setup, message = FALSE--------------------------------------------------- library(dplyr) library(SummarizedExperiment) library(LoomExperiment) library(hca) ## ---- eval = FALSE------------------------------------------------------------ # default_manifest_tbl <- hca::manifest() # default_manifest_tbl ## ----------------------------------------------------------------------------- manifest_filter <- hca::filters( projectId = list(is = "4a95101c-9ffc-4f30-a809-f04518a23803"), fileFormat = list(is = "loom"), workflow = list(is = c("optimus_v4.2.2", "optimus_v4.2.3")) ) ## ----------------------------------------------------------------------------- manifest_tibble <- hca::manifest(filters = manifest_filter) manifest_tibble ## ----------------------------------------------------------------------------- manifest_tibble |> dplyr::count(specimen_from_organism.organ) ## ----------------------------------------------------------------------------- manifest_tibble ## ----------------------------------------------------------------------------- file_uuid <- "24a8a323-7ecd-504e-a253-b0e0892dd730" ## ----------------------------------------------------------------------------- file_filter <- hca::filters( fileId = list(is = file_uuid) ) file_tbl <- hca::files(filters = file_filter) file_tbl ## ----------------------------------------------------------------------------- file_location <- file_tbl |> hca::files_download() file_location ## ----------------------------------------------------------------------------- loom <- LoomExperiment::import(file_location) metadata(loom) |> dplyr::glimpse() colData(loom) |> dplyr::as_tibble() |> dplyr::glimpse() ## ----------------------------------------------------------------------------- annotated_loom <- optimus_loom_annotation(file_location) annotated_loom ## new metadata setdiff( names(metadata(annotated_loom)), names(metadata(loom)) ) metadata(annotated_loom)$manifest ## new colData columns setdiff( names(colData(annotated_loom)), names(colData(loom)) ) ## ----sessionInfo-------------------------------------------------------------- sessionInfo()