Update Metadata in a MicrobiomeStat Data Object

Replaces or updates metadata from a file or data frame.

Usage

mStat_update_meta_data(
  data.obj,
  map.file,
  meta.sep = "\t",
  quote = "\"",
  comment = "",
  ...
)

Arguments

data.obj

A MicrobiomeStat data object, which is a list containing at minimum the following components:

• feature.tab: A matrix of feature abundances (taxa/genes as rows, samples as columns)

• meta.dat: A data frame of sample metadata (samples as rows)

Optional components include:

• feature.ann: A matrix/data frame of feature annotations (e.g., taxonomy)

• tree: A phylogenetic tree object (class "phylo")

• feature.agg.list: Pre-aggregated feature tables by taxonomy

Data objects can be created using converters like mStat_convert_phyloseq_to_data_obj or importers like mStat_import_qiime2_as_data_obj.

map.file

Path to metadata file (CSV/TSV) or a data frame.

meta.sep

Field separator (default tab).

quote

Quote character (default double quote).

comment

Comment character (lines starting with this are ignored).

...

Additional arguments passed to read.csv/read.table.

Value

A MicrobiomeStat data object with updated metadata.

Examples

if (FALSE) { # \dontrun{
  # Load required libraries
  library(vegan)
  data(peerj32.obj)

  # Update metadata using a CSV file
  # peerj32.obj <- mStat_update_meta_data(peerj32.obj, "metadata.csv")

  # Update metadata using a dataframe
  metadata <- data.frame(Treatment = sample(c("Control", "Treatment"),
                         length(colnames(peerj32.obj$feature.tab)), replace = TRUE))
  rownames(metadata) <- rownames(peerj32.obj$meta.dat)
  peerj32.obj <- mStat_update_meta_data(peerj32.obj, metadata)
} # }