classify_files: Classify FTMS files into categories based on filename...

In ume: Ultrahigh-Resolution Mass Spectrometry Data Evaluation for Complex Organic Matter

Classify FTMS files into categories based on filename patterns

Description

Classifies entries into categories (blank, standard, pool, sample, …) based on pattern rules applied to a specific search column. The identifiers returned in each category are also configurable.

Usage

classify_files(
  fi,
  search_col = "link_rawdata",
  id_col = "file_id",
  patterns = list(blank = c("blk", "blank", "MQ"), standard = c("srfa", "standard"), pool
    = c("pool")),
  include_blank_check = TRUE,
  return = c("list", "table")
)

Arguments

fi	data.table. Must contain the columns specified in search_col and id_col.
search_col	Character. Name of the column used for pattern matching. Defaults to "link_rawdata".
id_col	Character. Name of the column whose values are returned for each category. Defaults to "file_id".
patterns	Named list of character vectors. Each list entry is a category name, and its value is a vector of patterns.
include_blank_check	Logical; if TRUE and blank_check exists, it is used to assign "blank".
return	Either "list" (default) or "table". "list" → named list of ID vectors "table" → fi with added column category_analysis

Details

Default behavior:

• "blank": blank_check == "blank" or pattern "blk"

• "standard": pattern "srfa"

• "pool": pattern "pool"

• "sample": everything unmatched

Pattern matching is case-insensitive.

Value

Named list or a classified data.table.

Examples

# Minimal demo data
fi <- data.table::data.table(
  file_id       = 1:6,
  filename      = c("NS_blk_01.raw", "SRFA_20.raw", "Pool_A.raw",
                    "Sample_01.raw", "Sample_02.raw", "MQ_blank.raw"),
  blank_check   = c("blank", NA, NA, NA, NA, "blank"),  # optional column
  link_rawdata  = c("NS_blk_01.raw", "SRFA_20.raw", "Pool_A.raw",
                    "Sample_01.raw", "Sample_02.raw", "MQ_blank.raw")
)

# 1) Default behavior: return named list of file_ids by category
classify_files(fi)

# 2) Use a different column for pattern matching
classify_files(fi, search_col = "filename")

# 3) Return another ID field (here: file_id → stays the same for demo)
classify_files(fi, id_col = "file_id")

# 4) Return the full table with new category column
classify_files(fi, return = "table")

ume documentation built on Dec. 13, 2025, 1:06 a.m.