protti: create_queue – R documentation

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create_queue

Creates a mass spectrometer queue for Xcalibur

Description

This function creates a measurement queue for sample acquisition for the software Xcalibur. All possible combinations of the provided information will be created to make file and sample names.

Usage

create_queue(
  date = NULL,
  instrument = NULL,
  user = NULL,
  measurement_type = NULL,
  experiment_name = NULL,
  digestion = NULL,
  treatment_type_1 = NULL,
  treatment_type_2 = NULL,
  treatment_dose_1 = NULL,
  treatment_dose_2 = NULL,
  treatment_unit_1 = NULL,
  treatment_unit_2 = NULL,
  n_replicates = NULL,
  number_runs = FALSE,
  organism = NULL,
  exclude_combinations = NULL,
  inj_vol = NA,
  data_path = NA,
  method_path = NA,
  position_row = NA,
  position_column = NA,
  blank_every_n = NULL,
  blank_position = NA,
  blank_method_path = NA,
  blank_inj_vol = 1,
  export = FALSE,
  export_to_queue = FALSE,
  queue_path = NULL
)

Arguments

`date`	Optional, start date of the measurements.
`instrument`	Optional, instrument initials.
`user`	Optional, user name.
`measurement_type`	Optional, the measurement type of the samples (e.g "DIA", "DDA", "library" etc.).
`experiment_name`	Optional, name of the experiment.
`digestion`	Optional, the digestion types used in this experiment (e.g "LiP" and/or "tryptic control").
`treatment_type_1`	Optional, name of the treatment.
`treatment_type_2`	Optional, name of a second treatment that was combined with the first treatment.
`treatment_dose_1`	Optional, doses used for treatment 1. These can be concentrations or times etc.
`treatment_dose_2`	Optional, doses used for treatment 2. These can be concentrations or times etc.
`treatment_unit_1`	Optional, unit of the doses for treatment 1 (e.g min, mM, etc.).
`treatment_unit_2`	Optional, unit of the doses for treatment 2 (e.g min, mM, etc.).
`n_replicates`	Optional, number of replicates used per sample.
`number_runs`	Specifies if file names should be numbered from 1:n instead of adding experiment information. Default is FALSE.
`organism`	Optional, name of the organism used.
`exclude_combinations`	Optional, list of lists that contains vectors treatment types and treatment doses whos combinations should be excluded from the final queue.
`inj_vol`	The volume used for injection in microliter. Will be `NA` if not specified. Then it needs to be manually specified before the queue can be used.
`data_path`	The file path where the MS raw data should be saved. Backslashes should be escaped by another backslash. Will be `NA` if not specified, but needs to be specified later on then.
`method_path`	The file path of the MS acquisition method. Backslashes should be escaped by another backslash. Will be `NA` if not specified, but needs to be specified later on then.
`position_row`	The row positions that can be used for the samples (e.g c("A", "B")). If the number of specified rows and columns does not equal the total number of samples, positions will be repeated.
`position_column`	The column positions that can be used for the samples (e.g 8). If the number of specified rows and columns does not equal the total number of samples, positions will be repeated.
`blank_every_n`	Optional, specifies in which intervals a blank sample should be inserted.
`blank_position`	The plate position of the blank. Will be `NA` if not specified, but needs to be specified later on then.
`blank_method_path`	The file path of the MS acquisition method of the blank. Backslashes should be escaped by another backslash. Will be `NA` if not specified, but needs to be specified later on then.
`blank_inj_vol`	Injection volume of the blank sample. Will be `NA` if not specified, but needs to be specified later on then.
`export`	Logical, specifying if queue should be exported from R and saved as a .csv file. Default is TRUE. Further options for export can be adjusted with the `export_to_queue` and `queue_path` arguments.
`export_to_queue`	Logical, specifying if the resulting queue should be appended to an already existing queue. If false result will be saved as `queue.csv`.
`queue_path`	Optional, file path to a queue file to which the generated queue should be appended if `export_to_queue = TRUE`. If not specified queue file can be chosen interactively.

Value

If export_to_queue = FALSE a file named queue.csv will be returned that contains the generated queue. If export_to_queue = TRUE, the resulting generated queue will be appended to an already existing queue that needs to be specified either interactively or through the argument queue_path.

Examples

create_queue(
  date = c("200722"),
  instrument = c("EX1"),
  user = c("jquast"),
  measurement_type = c("DIA"),
  experiment_name = c("JPQ031"),
  digestion = c("LiP", "tryptic control"),
  treatment_type_1 = c("EDTA", "H2O"),
  treatment_type_2 = c("Zeba", "unfiltered"),
  treatment_dose_1 = c(10, 30, 60),
  treatment_unit_1 = c("min"),
  n_replicates = 4,
  number_runs = FALSE,
  organism = c("E. coli"),
  exclude_combinations = list(list(
    treatment_type_1 = c("H2O"),
    treatment_type_2 = c("Zeba", "unfiltered"),
    treatment_dose_1 = c(10, 30)
  )),
  inj_vol = c(2),
  data_path = "D:\\2007_Data",
  method_path = "C:\\Xcalibur\\methods\\user\\DIA_120min_41var_AGC200",
  position_row = c("A", "B", "C", "D", "E", "F"),
  position_column = 8,
  blank_every_n = 4,
  blank_position = "1-V1",
  blank_method_path = "C:\\Xcalibur\\methods\\blank"
)

protti

Bottom-Up Proteomics and LiP-MS Quality Control and Data Analysis Tools

v0.1.1

MIT + file LICENSE

Authors

Jan-Philipp Quast [aut, cre], Dina Schuster [aut], ETH Zurich [cph, fnd]

Initial release