Load cached files into R as a merged TreeSummarizedExperiment object — loadMetagenomicData • parkinsonsMetagenomicData

'loadMetagenomicData' takes a table of information about cached files, including paths to the cached files as well as associated UUIDs and data types, and loads the files into R as TreeSummarizedExperiment objects. Associated sample metadata is automatically attached as colData, and the objects are merged into a single TreeSummarizedExperiment object.

Usage

loadMetagenomicData(cache_table)

Arguments

cache_table: A data.frame or tibble: structured like cacheMetagenomicData() output; contains the columns 'uuid', 'cache_path', and 'data_type', with appropriate entries for each file to be loaded in.

Value

A TreeSummarizedExperiment object with relevant sample metadata attached as colData.

Details

At the moment, only the metaphlan_lists data types, viral_clusters and relative_abundance, as well as the humann data types, have parsing functions for automatically loading into TreeSummarizedExperiment objects.

Examples

if (FALSE) { # \dontrun{
if(interactive()){
 cache_table <- cacheMetagenomicData(uuid = "004c5d07-ec87-40fe-9a72-6b23d6ec584e",
                                     data_type = "relative_abundance")
 loadMetagenomicData(cache_table = cache_table)
 }
} # }