Package 'SpectraToQueries'

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

Examples

NULL

---

Filter matrix

Description

Filter matrix

Usage

filter_matrix(matrix, n)

Arguments

matrix	Matrix
n	N

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 mzs
dalton	dalton
ppm	PPM
decimals	decimals

Examples

NULL

---

Generate combinations

Description

Generate combinations

Usage

generate_combinations(x, max_ions)

Arguments

x	x
max_ions	Max ions

Examples

NULL

---

Perform list of queries (progress)

Description

Perform list of queries (progress)

Usage

generate_combinations_progress(indices, ions_list, max_ions)

Arguments

indices	Indices
ions_list	Ions list
max_ions	Max ions

Examples

NULL

---

Harmonize mzs

Description

Harmonize mzs

Usage

harmonize_mzs(spectra, dalton, ppm)

Arguments

spectra	Spectra
dalton	Dalton
ppm	PPM

Examples

NULL

---

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, spectra, dalton = 0.01, ppm = 25)

Arguments

index	Index
ions_list	Ions list
spectra	Spectra
dalton	Dalton
ppm	PPM

Examples

NULL

---

Perform list of queries (progress)

Description

Perform list of queries (progress)

Usage

perform_list_of_queries_progress(
  indices,
  ions_list,
  spectra,
  dalton = 0.01,
  ppm = 25
)

Arguments

indices	Indices
ions_list	Ions list
spectra	Spectra
dalton	Dalton
ppm	PPM

Examples

NULL

---

Perform query

Description

Perform query

Usage

perform_query(spectra, frags, nls, dalton = 0.01, ppm = 25)

Arguments

spectra	Spectra
frags	Fragments
nls	Neutral losses
dalton	Dalton
ppm	PPM

Examples

NULL

---

Spectra to queries

Description

This function converts spectra to queries.

Usage

spectra_to_queries(
  spectra = NULL,
  export = "data/interim/queries.tsv",
  beta = 0.5,
  dalton = 0.01,
  decimals = 4L,
  intensity_min = 0L,
  ions_max = 10L,
  n_skel_min = 5L,
  n_spec_min = 3L,
  ppm = 20L,
  senspe_min = 0.1,
  sensitivity_min = 0L,
  specificity_min = 0L,
  zero_val = 0L
)

Arguments

spectra	Spectra path
export	Export path
beta	Beta parameter of the F-score calculation
dalton	Tolerance in Dalton. Default to 0.01
decimals	Number of decimals for rounding. Default to 4
intensity_min	Minimal intensity. Default to 0
ions_max	Maximal number of ions in the query. Default to 10
n_skel_min	Minimal number of individuals per skeleton. Default to 5
n_spec_min	Minimal number of individuals where a signal has to be found. Default to 3
ppm	Tolerance in parts per million Default to 25
senspe_min	Minimal product of inner and outer ratios. Default to 0.1
sensitivity_min	Minimal sensitivity. Default to 0.3
specificity_min	Minimal specificity. Default to 0
zero_val	Zero value for intensity. Default to 0

Value

A file with diagnostic query ions

Examples

NULL

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