## ----include = FALSE---------------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, message = FALSE, warning = FALSE, comment = "#>", fig.path = "man/figures/", out.width = "100%" ) ## ----eval = FALSE------------------------------------------------------------- # if (!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # # BiocManager::install("clustifyrdatahub") ## ----------------------------------------------------------------------------- knitr::kable(dplyr::select( read.csv(system.file("extdata", "metadata.csv", package = "clustifyrdatahub")), c(1, 9, 2:7))) ## ----------------------------------------------------------------------------- library(ExperimentHub) eh <- ExperimentHub() ## query refs <- query(eh, "clustifyrdatahub") refs ## either by index or id ref_hema_microarray <- refs[[7]] ## load the first resource in the list ref_hema_microarray <- refs[["EH3450"]] ## load by EH id ## or list and load refs <- listResources(eh, "clustifyrdatahub") ref_hema_microarray <- loadResources( eh, "clustifyrdatahub", "ref_hema_microarray" )[[1]] ## use for classification of cell types res <- clustifyr::clustify( input = clustifyr::pbmc_matrix_small, metadata = clustifyr::pbmc_meta$classified, ref_mat = ref_hema_microarray, query_genes = clustifyr::pbmc_vargenes ) ## ----------------------------------------------------------------------------- ## or load refs by function name (after loading hub library) library(clustifyrdatahub) ref_hema_microarray()[1:5, 1:5] ## data are loaded ref_hema_microarray(metadata = TRUE) ## only metadata ## ----------------------------------------------------------------------------- sessionInfo()