Import normalized matrices into a SummarizedExperiment

Reads all TSV files matching a pattern from a directory, one assay per file. Each TSV must have column 1 named ProteinGroups and remaining columns as sample names matching the sample_col in the metadata file.

Usage

import_norm_matrices(
  tsv_dir,
  metadata_path,
  pattern = "matrix_log2_.*\\.tsv$",
  method_names = NULL,
  condition_col = "Condition",
  sample_col = "Column"
)

Arguments

tsv_dir

Character. Directory containing the normalized TSV files.

metadata_path

Character. Path to a TSV or CSV file with at minimum columns sample_col and condition_col.

pattern

Character. Regex to filter files in tsv_dir. Default: "matrix_log2_.*\\.tsv$".

method_names

Character vector. Assay names to assign (in order). NULL (default) = extracted from file names between matrix_log2_ and .tsv.

condition_col

Character. Column in metadata with condition/group labels.

sample_col

Character. Column in metadata with sample names.

Value

A SummarizedExperiment with one assay per TSV, colData from metadata, and rowData containing Protein.IDs.

Examples

data(nadia_dia)
se <- nm_prepare_se(nadia_dia, verbose = FALSE)
se <- nm_run_normalizations(se, methods = c("cycloess", "MAD"), verbose = FALSE)

# Write the normalized assays as TSVs, then read them back into a new SE
tsv_dir <- file.path(tempdir(), "nm_matrices")
dir.create(tsv_dir, showWarnings = FALSE)
for (a in c("cycloess", "MAD")) {
  m <- SummarizedExperiment::assay(se, a)
  utils::write.table(
    data.frame(ProteinGroups = rownames(m), m, check.names = FALSE),
    file.path(tsv_dir, paste0("matrix_log2_", a, ".tsv")),
    sep = "\t", row.names = FALSE, quote = FALSE)
}
meta_path <- file.path(tsv_dir, "metadata.tsv")
utils::write.table(as.data.frame(SummarizedExperiment::colData(se)), meta_path,
                   sep = "\t", row.names = FALSE, quote = FALSE)

se_nm <- import_norm_matrices(tsv_dir, meta_path)
#> import_norm_matrices: loaded 2 assay(s) -- MAD, cycloess
#>   Proteins: 1997 | Samples: 12
SummarizedExperiment::assayNames(se_nm)
#> [1] "MAD"      "cycloess"