## ---- include = FALSE--------------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) ## ----installation, eval=FALSE------------------------------------------------- # ## Install BioConductor if not installed # if (!require("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # # ## Release version (not yet in Bioc, so it doesn't work yet) # BiocManager::install("MicrobiomeBenchmarkData") # # ## Development version # BiocManager::install("waldronlab/MicrobiomeBenchmarkData") ## ---- message=FALSE----------------------------------------------------------- library(MicrobiomeBenchmarkData) library(purrr) ## ----------------------------------------------------------------------------- data('sampleMetadata', package = 'MicrobiomeBenchmarkData') ## Get columns present in all samples sample_metadata <- sampleMetadata |> discard(~any(is.na(.x))) |> head() knitr::kable(sample_metadata) ## ----------------------------------------------------------------------------- dats <- getBenchmarkData() ## ----------------------------------------------------------------------------- dats ## ----------------------------------------------------------------------------- tse <- getBenchmarkData('HMP_2012_16S_gingival_V35_subset', dryrun = FALSE)[[1]] tse ## ----------------------------------------------------------------------------- list_tse <- getBenchmarkData(dats$Dataset[2:4], dryrun = FALSE) str(list_tse, max.level = 1) ## ----------------------------------------------------------------------------- mbd <- getBenchmarkData(dryrun = FALSE) str(mbd, max.level = 1) ## ----------------------------------------------------------------------------- ## In the case, the column is named as taxon_annotation tse <- mbd$HMP_2012_16S_gingival_V35_subset rowData(tse) ## ---- eval=FALSE-------------------------------------------------------------- # removeCache() ## ----------------------------------------------------------------------------- sessionInfo()