Package 'SpectraToQueries'

Combine ions into minimal AND/OR expression with sorting

Description

Combine ions into minimal AND/OR expression with sorting

Usage

combine_ions_minimal(ion_lists)

Arguments

ion_lists

List of character vectors representing ion combinations

Value

Single character string representing nested AND/OR expression

---

Check if spectrum contains all target m/z values

Description

Check if spectrum contains all target m/z values

Usage

contains_all_mz(spec_mz, target_mz, dalton, ppm)

Arguments

spec_mz	Numeric vector of spectrum m/z values
target_mz	Numeric vector of target m/z values to find
dalton	Tolerance in Dalton
ppm	Tolerance in parts per million

Value

Logical indicating if all targets are found

Examples

NULL

---

Check if spectrum contains all target m/z values (internal variant with pre-computed tolerances)

Description

Check if spectrum contains all target m/z values (internal variant with pre-computed tolerances)

Usage

contains_all_mz_tol(spec_mz, target_mz, tol)

Arguments

spec_mz	Numeric vector of spectrum m/z values
target_mz	Numeric vector of target m/z values to find
tol	Numeric vector of pre-computed tolerances (length must match target_mz)

Value

Logical indicating if all targets are found

Examples

NULL

---

Create directory

Description

This function creates a directory at the specified path if it does not already exist.

Usage

create_dir(export)

Arguments

export

Path to the directory to be created

Value

Message indicating the status of directory creation

Source

https://github.com/taxonomicallyinformedannotation/tima/blob/main/R/create_dir.R

---

Create matrix

Description

Create matrix

Usage

create_matrix(spectra, zero_val = 0, name)

Arguments

spectra	Spectra
zero_val	Zero value
name	Name

Value

A matrix with spectra intensity data

Examples

NULL

---

Filter matrix

Description

Filter matrix

Usage

filter_matrix(matrix, n)

Arguments

matrix	Matrix to filter
n	Minimum number of non-zero values per column

Value

Filtered matrix with columns having at least n non-zero values

Examples

NULL

---

Fix binned mzs

Description

Fix binned mzs

Usage

fix_binned_mzs(binned_m, original_mzs, dalton, ppm, decimals)

Arguments

binned_m	Binned matrix
original_mzs	Original m/z values from spectra
dalton	Tolerance in Dalton
ppm	Tolerance in parts per million
decimals	Number of decimal places for rounding

Value

Matrix with corrected m/z column names

Examples

NULL

---

Generate combinations

Description

Generate combinations

Usage

generate_combinations(x, max_ions)

Arguments

x	Vector of elements to combine
max_ions	Maximum number of ions in combinations

Value

List of all combinations

Examples

NULL

---

Generate combinations with progress

Description

Generate combinations with progress

Usage

generate_combinations_progress(
  indices,
  ions_list,
  max_ions,
  show_progress = TRUE
)

Arguments

indices	Vector of indices to process
ions_list	List of ions for each index
max_ions	Maximum number of ions in combinations
show_progress	Logical: show progress bar (default TRUE)

Value

List of all combinations for each index

Examples

NULL

---

Harmonize mzs

Description

Harmonize mzs

Usage

harmonize_mzs(spectra, dalton, ppm)

Arguments

spectra	Spectra object
dalton	Tolerance in Dalton
ppm	Tolerance in parts per million

Value

Spectra with harmonized m/z values

Examples

NULL

---

Example mass spectrometry spectra from MIADB (as portable data.frame)

Description

A data.frame containing 321 spectra of monoterpene indole alkaloids (MIAs) from the MIADB (Monoterpene Indole Alkaloid Database). This is stored as a portable data.frame with m/z and intensity peaks as list columns, and is automatically converted to a Spectra object when used in spectra_to_queries().

Usage

mia_spectra_df

Format

A data.frame with 321 rows and 37 columns:

• Metadata columns: msLevel, rtime, acquisitionNum, TITLE, PRECURSOR_MZ, SKELETON, and other MS/MS spectrum attributes

• mz (list): Fragment m/z values for each spectrum

• intensity (list): Fragment intensities for each spectrum

Total of approximately 48,510 peaks across all spectra.

Details

The mia_spectra_df object represents the raw spectral data with minimal preprocessing. Use mia_spectra_grouped_df for the pre-grouped variant.

This portable data.frame format enables export to CSV, Parquet, JSON, and other formats for cross-platform distribution via r-universe. It is automatically converted to a Spectra object by spectra_to_queries().

Source

Data extracted from MIADB, a public spectral library of monoterpene indole alkaloids. Original source: https://miadb.imsb.qcb.usp.br/

Accompanying publication: Szwarc, S., Rutz, A., Lee, K. et al. (2025). "Translating community-wide spectral library into actionable chemical knowledge: a proof of concept with monoterpene indole alkaloids." Journal of Cheminformatics, 17:62. https://doi.org/10.1186/s13321-025-01009-0

Examples

## Not run: 
  # Load the raw spectra
  utils::data(mia_spectra_df)
  nrow(mia_spectra_df)  # 321 spectra

  # Convert to Spectra object (for advanced users)
  # spectra_obj <- SpectraToQueries:::df_to_spectra(mia_spectra_df)

## End(Not run)

---

Grouped mass spectrometry spectra from MIADB (as portable data.frame)

Description

A data.frame containing 321 grouped mass spectra from the MIADB (Monoterpene Indole Alkaloid Database), combined by spectrum title. This is the primary example dataset used in the spectra_to_queries() function. Stored as a portable data.frame with m/z and intensity peaks as list columns.

Usage

mia_spectra_grouped_df

Format

A data.frame with 321 rows and 36 columns:

• Metadata columns: msLevel, rtime, acquisitionNum, TITLE, PRECURSOR_MZ, SKELETON, and other MS/MS spectrum attributes

• mz (list): Fragment m/z values for each spectrum

• intensity (list): Fragment intensities for each spectrum

Total of approximately 48,510 peaks across all spectra (median ~132 peaks per spectrum).

Details

This dataset is grouped by spectrum title (via Spectra::combineSpectra()) to simplify downstream analysis. It is the recommended example for demonstrating the spectra_to_queries() workflow.

This portable data.frame format enables export to CSV, Parquet, JSON, and other formats for cross-platform distribution via r-universe. It is automatically converted to a Spectra object by spectra_to_queries().

Source

Data extracted and pre-grouped from MIADB, a public spectral library of monoterpene indole alkaloids. Original source: https://miadb.imsb.qcb.usp.br/

Accompanying publication: Szwarc, S., Rutz, A., Lee, K. et al. (2025). "Translating community-wide spectral library into actionable chemical knowledge: a proof of concept with monoterpene indole alkaloids." Journal of Cheminformatics, 17:62. https://doi.org/10.1186/s13321-025-01009-0

Examples

## Not run: 
  # Load the grouped spectra
  utils::data(mia_spectra_grouped_df)
  nrow(mia_spectra_grouped_df)  # 321 spectra
  table(mia_spectra_grouped_df$SKELETON)  # Skeleton distribution

  # Convert to Spectra object (for advanced users)
  # spectra_obj <- SpectraToQueries:::df_to_spectra(mia_spectra_grouped_df)

## End(Not run)

---

Normalize peaks

Description

Normalize peaks

Usage

normalize_peaks()

Examples

NULL

---

Perform list of queries

Description

Perform list of queries

Usage

perform_list_of_queries(index, ions_list, query_data, dalton, ppm)

Arguments

index	Index of the ion list to process
ions_list	List of ions for queries
query_data	Data frame with columns mz, precursor_mz, and skeleton
dalton	Tolerance in Dalton
ppm	Tolerance in parts per million

Value

Data frame with target and value columns

Examples

NULL

---

Perform list of queries

Description

Perform list of queries

Usage

perform_list_of_queries_progress(
  ions_list,
  spectra,
  dalton,
  ppm,
  show_progress = TRUE
)

Arguments

ions_list	List of ion combinations for queries
spectra	Spectra object to search
dalton	Tolerance in Dalton
ppm	Tolerance in parts per million
show_progress	Logical: show progress bar (default TRUE)

Value

List of query results

Examples

NULL

---

Perform query

Description

Perform query

Usage

perform_query(all_mz, precursor_mz, frags, nls, dalton, ppm)

Arguments

all_mz	List of numeric vectors of m/z values for each spectrum
precursor_mz	Numeric vector of precursor m/z values for each spectrum
frags	Fragment masses to search for
nls	Neutral losses to search for
dalton	Tolerance in Dalton
ppm	Tolerance in parts per million

Value

Filtered spectra object

Examples

NULL

---

Prepare spectra data for querying

Description

Extracts mz, precursor m/z, and skeleton labels once, so perform_query() never has to touch the Spectra backend again.

Usage

prepare_query_data(spectra)

Arguments

spectra

Spectra object

Examples

NULL

---

Spectra to queries

Description

This function converts spectra to diagnostic ion queries.

Usage

spectra_to_queries(
  spectra = NULL,
  export = "data/interim/queries.tsv",
  dalton = 0.01,
  decimals = 4L,
  intensity_min = 0,
  ions_max = 10L,
  n_skel_min = 5L,
  n_spec_min = 3L,
  ppm = 30,
  mcc_min = 0,
  precision_min = 0,
  recall_min = 0,
  zero_val = 0
)

Arguments

spectra	Spectra object or path to MGF file. If NULL, loads the example spectra dataset. If the string "grouped", loads the grouped example spectra. Otherwise, a path to an MGF file or a Spectra object.
export	Export path
dalton	Tolerance in Dalton. Default to 0.01
decimals	Number of decimals for rounding. Default to 4L
intensity_min	Minimal intensity. Default to 0.0
ions_max	Maximal number of ions in the query. Default to 10L
n_skel_min	Minimal number of individuals per skeleton. Default to 5L
n_spec_min	Minimal number of individuals where a signal has to be found. Default to 3L
ppm	Tolerance in parts per million Default to 30.0
mcc_min	Minimal single-ion Matthews Correlation Coefficient. Default to 0.0
precision_min	Minimal single ion precision (pre-filter before MCC). Default to 0.0
recall_min	Minimal single ion recall (pre-filter before MCC). Default to 0.0
zero_val	Zero value for intensity. Default to 0.0

Value

A file with diagnostic query ions

Examples

## Not run: 
  # Run with default spectra
  spectra_to_queries()

  # Or explicitly load and pass spectra_grouped
  data(spectra_grouped)
  spectra_to_queries(spectra = spectra_grouped)

## End(Not run)

---