Loading, filtering and reformatting of MS DIA data from Spectronaut

Read a data file from Spectronaut, apply filtering conditions, select columns necessary for analysis, and return the reformatted data.

Usage

preprocessing(
  fileName,
  dataSet = NULL,
  filterNaN = TRUE,
  filterUnique = 2,
  replaceBlank = TRUE,
  saveRm = TRUE
)

Arguments

fileName

The name of the .csv file containing MS data (including the path to the file, if needed).

dataSet

The raw data set, if already loaded in R.

filterNaN

A boolean (default = TRUE) specifying whether observations including NaN should be omitted.

filterUnique

An integer (default = 2) specifying how many number of unique peptides are required to include a protein.

replaceBlank

A boolean (default = TRUE) specifying whether proteins without names should be be named by their accession numbers.

saveRm

A boolean (default = TRUE) specifying whether to save removed data to current working directory.

Value

A 2d dataframe.

Details

The function executes the following:

1. Reads the file.

2. Applies applicable filters, if necessary.

3. Provides summary statistics and a histogram of all values reported in the data set.

4. Selects columns that contain necessary information for the analysis.

5. Re-formats the data to present individual proteins as columns and group replicates under each protein.

6. Stores the data as a data.frame and prints the levels of condition and replicate to the user.