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TARDIS Peak Detection

tardisPeaks.Rd

Main function of the TARDIS package that is called in the Shiny app. Given data files and a list of targeted compounds it returns the area of those peaks, optional diagnostic plots and several other parameters. See vignette for a detailed tutorial.

Usage

tardisPeaks(
  file_path = NULL,
  lcmsData = NULL,
  dbData,
  ppm = 5,
  rtdev = 18,
  mass_range = NULL,
  polarity = "positive",
  output_directory,
  plots_samples = FALSE,
  plots_QC = FALSE,
  diagnostic_plots = TRUE,
  batch_positions,
  QC_pattern = "QC",
  sample_pattern = "",
  rt_alignment = TRUE,
  int_std_id,
  screening_mode = FALSE,
  smoothing = TRUE,
  max_int_filter = NULL
)

Arguments

file_path

character(1) Path to the .mzML or .mzXML files containing LC-MS data.

lcmsData

MsExperiment MsExperiment containing the data to be preprocessed. Sampledata should at least include run type and should match the later provided "QC" or "sample" pattern.

dbData

Output of createTargetList()

ppm

numeric(1) Allowed deviance from given m/z of targets in ppm.

rtdev

numeric(1) Allowed deviance from given retention time of compound, defines search window for the peak picking algorithm.

mass_range

numeric(2) If the user uses data with overlapping mass windows, only one mass window at the time can be analyzed, specify this here.

polarity

character(1) Ionisation mode to be considered, can be either "positive" or "negative"

output_directory

character(1) Provide directory to store output

plots_samples

logical(1) Create plots for all samples

plots_QC

logical(1) Create plots for all QCs

diagnostic_plots

logical(1) Create diagnostic plots of 5 QCs spread across the runs

batch_positions

list Indicate start and end file of each batch, e.g. list(c(1,20),c(21,40))

QC_pattern

character(1) Pattern of QC files

sample_pattern

character(1) Pattern of sample files

rt_alignment

logical(1) Align retention time based on internal standard compounds in the QC samples.

int_std_id

character Provide ID's of internal standard compounds for retention time alignment

screening_mode

logical(1) Run the algorithm over 5 QCs to quickly check retention time shifts

smoothing

logical(1) Smooth the peaks with sgolayfilt()

max_int_filter

numeric(1) Disregard peaks with a max. int. lower than this value

Value

returns list with auc table and feature table with summarized stats per compound. Outputs plots and other tables to output folder.