Add sample metadata to TreeSummarizedExperiment object as colData

'add_metadata' uses the IDs of samples included in a TreeSummarizedExperiment object to attach sample metadata as colData. This new metadata can combine with pre-existing colData.

Usage

add_metadata(sample_ids, id_col = "uuid", experiment, method = "append")

Arguments

sample_ids

Vector of strings: sample IDs, such as UUIDs, that will be used to attach samples to their sampleMetadata

id_col

String: column name within sampleMetadata where 'sample_ids' will be found, Default: 'uuid'

experiment

TreeSummarizedExperiment object: contains samples to add metadata to

method

String: 'append', 'overwrite', or 'ignore', indicating how to handle duplicate colData columns, Default: 'append'

Value

TreeSummarizedExperiment object with sampleMetadata stored as colData

Details

sampleMetadata columns found to have the same name as pre-existing colData columns can be either appended (preserving both duplicate columns), used to overwrite the pre-existing columns (leaving only the new version of the duplicate columns), or ignored (leaving only the old version of the duplicate columns)

See also

DataFrame-class, S4VectorsOverview TreeSummarizedExperiment-class

Examples

if (FALSE) { # \dontrun{
if(interactive()){
 fpath <- file.path(system.file("extdata",
                                package = "parkinsonsMetagenomicData"),
                    "sample_experiment.Rds")
 sample_experiment <- readRDS(fpath)

 add_metadata(sample_ids = colnames(sample_experiment),
              id_col = "uuid",
              experiment = sample_experiment)
 }
} # }