Creates a mass spectrometer queue for Xcalibur

Source: R/create_queue.R

[Experimental] 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.

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, character value indicating the start date of the measurements.

instrument

optional, character value indicating the instrument initials.

user

optional, character value indicating the user name.

measurement_type

optional, character value indicating the measurement type of the samples (e.g "DIA", "DDA", "library" etc.).

experiment_name

optional, character value indicating the name of the experiment.

digestion

optional, character vector indicating the digestion types used in this experiment (e.g "LiP" and/or "tryptic control").

treatment_type_1

optional, character vector indicating the name of the treatment.

treatment_type_2

optional, character vector indicating the name of a second treatment that was combined with the first treatment.

treatment_dose_1

optional, numeric vector indicating the doses used for treatment 1. These can be concentrations or times etc.

treatment_dose_2

optional, numeric vector indicating the doses used for treatment 2. These can be concentrations or times etc.

treatment_unit_1

optional, character vector indicating the unit of the doses for treatment 1 (e.g min, mM, etc.).

treatment_unit_2

optional, character vector indicating the unit of the doses for treatment 2 (e.g min, mM, etc.).

n_replicates

optional, a numeric value indicating the number of replicates used per sample.

number_runs

a logical that specifies if file names should be numbered from 1:n instead of adding experiment information. Default is FALSE.

organism

optional, character value indicating the name of the organism used.

exclude_combinations

optional, list of lists that contains vectors of treatment types and treatment doses of which combinations should be excluded from the final queue.

inj_vol

a numeric value indicating 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

a character value indicating 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

a character value indicating 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

a character vector that contains 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

a character vector that contains 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, numeric value that specifies in which intervals a blank sample should be inserted.

blank_position

a character value that specifies the plate position of the blank. Will be NA if not specified, but needs to be specified later on then.

blank_method_path

a character value that specifies 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

a numeric value that specifies the injection volume of the blank sample. Will be NA if not specified, but needs to be specified later on then.

export

a logical value that specifies if the 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

a logical value that specifies if the resulting queue should be appended to an already existing queue. If false result will be saved as queue.csv.

queue_path

optional, a character value that specifies the 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\\DIA_120min",
  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"
)
#> # A tibble: 80 × 21
#>    `Sample Type` `File Name`               `Sample ID` Path  `Instrument Method`
#>    <chr>         <chr>                           <dbl> <chr> <chr>              
#>  1 QC            200722_EX1_jquast_blank_1           1 "D:\… "C:\\Xcalibur\\met…
#>  2 Unknown       200722_EX1_jquast_DIA_JP…           1 "D:\… "C:\\Xcalibur\\met…
#>  3 Unknown       200722_EX1_jquast_DIA_JP…           1 "D:\… "C:\\Xcalibur\\met…
#>  4 Unknown       200722_EX1_jquast_DIA_JP…           1 "D:\… "C:\\Xcalibur\\met…
#>  5 Unknown       200722_EX1_jquast_DIA_JP…           1 "D:\… "C:\\Xcalibur\\met…
#>  6 QC            200722_EX1_jquast_blank_2           1 "D:\… "C:\\Xcalibur\\met…
#>  7 Unknown       200722_EX1_jquast_DIA_JP…           1 "D:\… "C:\\Xcalibur\\met…
#>  8 Unknown       200722_EX1_jquast_DIA_JP…           1 "D:\… "C:\\Xcalibur\\met…
#>  9 Unknown       200722_EX1_jquast_DIA_JP…           1 "D:\… "C:\\Xcalibur\\met…
#> 10 Unknown       200722_EX1_jquast_DIA_JP…           1 "D:\… "C:\\Xcalibur\\met…
#> # ℹ 70 more rows
#> # ℹ 16 more variables: `Process Method` <lgl>, `Calibration File` <lgl>,
#> #   Position <chr>, `Inj Vol` <dbl>, Level <lgl>, `Sample Wt` <dbl>,
#> #   `Sample Vol` <dbl>, `ISTD Amt` <dbl>, `Dil Factor` <dbl>, `L1 Study` <lgl>,
#> #   `L2 Client` <lgl>, `L3 Laboratory` <lgl>, `L4 Company` <lgl>,
#> #   `L5 Phone` <lgl>, Comment <lgl>, `Sample Name` <chr>