randomise_queue: Randomise samples in MS queue

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

Randomise samples in MS queue

Description

This function randomises the order of samples in an MS queue. QC and Blank samples are left in place. It is also possible to randomise only parts of the queue. Before running this make sure to set a specific seed with the set.seed() function. This ensures that the randomisation of the result is consistent if the function is run again.

Usage

randomise_queue(data = NULL, rows = NULL, export = FALSE)

Arguments

data	optional, a data frame that contains a queue. If not provided a queue file can be chosen interactively.
rows	optional, a numeric vector that specifies a range of rows in for which samples should be randomized.
export	a logical value that determines if a "randomised_queue.csv" file will be saved in the working directory. If FALSE a data frame will be returned.

Value

If export = TRUE a "randomised_queue.csv" file will be saved in the working directory. If export = FALSE a data frame that contains the randomised queue is returned.

Examples

queue <- 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"
)

head(queue, n = 20)

randomised_queue <- randomise_queue(
  data = queue,
  export = FALSE
)

head(randomised_queue, n = 20)

protti documentation built on Jan. 22, 2023, 1:11 a.m.