Update Metadata in a MicrobiomeStat Data Object — mStat_update_meta

This function updates the metadata in a MicrobiomeStat data object. It either reads the metadata from a file (CSV or tab-delimited) or directly uses an input dataframe.

Usage

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

Arguments

data.obj: A list object in a format specific to MicrobiomeStat, which can include components such as feature.tab (matrix), feature.ann (matrix), meta.dat (data.frame), tree, and feature.agg.list (list). The data.obj can be converted from other formats using several functions from the MicrobiomeStat package, including: 'mStat_convert_DGEList_to_data_obj', 'mStat_convert_DESeqDataSet_to_data_obj', 'mStat_convert_phyloseq_to_data_obj', 'mStat_convert_SummarizedExperiment_to_data_obj', 'mStat_import_qiime2_as_data_obj', 'mStat_import_mothur_as_data_obj', 'mStat_import_dada2_as_data_obj', and 'mStat_import_biom_as_data_obj'. Alternatively, users can construct their own data.obj. Note that not all components of data.obj may be required for all functions in the MicrobiomeStat package.
map.file: a character string or dataframe. The path to the metadata file (CSV or TSV) or a dataframe containing the metadata.
meta.sep: a character string. The field separator character in the metadata file. Default is a tab ("\t").
quote: a character string. The set of quoting characters for the metadata file. Default is a double quote ('"').
comment: a character string. The comment character for the metadata file. Lines beginning with this character are ignored.
...: further arguments to be passed to the read.csv or read.table function.

Value

a list. An updated MicrobiomeStat data object that includes the new meta.dat.

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)
} # }