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Mass Combine

Source: R/mass_combine.R
mass_combine.Rd

Combines two massSight objects by aligning their features and correcting for systematic differences in retention time and mass-to-charge ratios.

Usage

mass_combine(
  ms1,
  ms2,
  optimize = TRUE,
  rt_delta = 0.5,
  mz_delta = 15,
  minimum_intensity = 10,
  iso_method = "manual",
  eps = 0.1,
  rt_iso_threshold = 0.01,
  mz_iso_threshold = 2,
  match_method = "unsupervised",
  smooth_method = "gam",
  weights = c(1, 1, 1),
  log = NULL,
  output = NULL,
  n_iter = 50,
  ...
)

Arguments

ms1

A massSight object representing the results of a preprocessed LC-MS experiment that will serve as the reference dataset.

ms2

A massSight object representing the results of a second preprocessed LC-MS experiment that will be aligned to ms1.

optimize

Logical: whether to optimize alignment parameters using known metabolites. Default is TRUE

rt_delta

Numeric: the retention time window (+/-) in minutes to consider when aligning features. Default is 0.5.

mz_delta

Numeric: the mass-to-charge ratio window (+/-) in ppm to consider when aligning features. Default is 15.

minimum_intensity

Numeric: the minimum intensity threshold for features to be considered in the alignment. Default is 10.

iso_method

Character: the method for isolating high-quality features before modeling drift. Options are "manual" or "dbscan". Default is "manual".

eps

Numeric: epsilon parameter for DBSCAN clustering when iso_method = "dbscan". Default is 0.1.

rt_iso_threshold

Numeric: the retention time similarity threshold for manual isolation. Default is 0.01.

mz_iso_threshold

Numeric: the m/z similarity threshold for manual isolation. Default is 2.

match_method

Character: the method for initial feature matching. Options are "unsupervised" (uses all features) or "supervised" (uses only known metabolites). Default is "unsupervised".

smooth_method

Character: the method for smoothing systematic drift. Options are "gam", "bayesian_gam", or "gp". Default is "gam".

weights

Numeric vector: weights for RT, m/z, and intensity in the alignment scoring. Default is c(1, 1, 1).

log

Character: path to save the log file. Set to NULL to disable logging. Default is NULL.

output

Character: directory to save output files. Default is NULL (current directory).

n_iter

Integer: number of optimization iterations if optimize=TRUE. Default is 50.

...

Additional arguments passed to internal functions.

Value

A MergedMSObject containing:

  • Original ms1 and ms2 objects

  • Matched features between datasets

  • Drift correction models

  • Alignment quality metrics

Examples

if (FALSE) { # \dontrun{
# Basic usage with default parameters
combined <- mass_combine(ms1_data, ms2_data)

# Use optimization with known metabolites
combined <- mass_combine(ms1_data, ms2_data,
                        optimize = TRUE,
                        n_iter = 50)

# Custom parameters for stricter matching
combined <- mass_combine(ms1_data, ms2_data,
                        rt_delta = 0.3,
                        mz_delta = 10,
                        minimum_intensity = 100)
} # }