Skip to contents

Loading and reformatting of MS data from Scaffold

Source: R/preprocessing.R
preprocessing_scaffold.Rd

Read a data file from Scaffold, select columns necessary for analysis, and return the reformatted data.

Usage

preprocessing_scaffold(fileName, dataSet = NULL, zeroNA = TRUE, oneNA = TRUE)

Arguments

fileName

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

dataSet

The raw data set, if already loaded in R.

zeroNA

A boolean (default = TRUE) specifying whether 0's should be converted to NA's.

oneNA

A boolean (default = TRUE) specifying whether 1's should be converted to NA's.

Value

  • If the data contains columns for Gene Ontology (GO) annotation terms, the function returns a list containing both the preprocessed 2d dataframe and a list of GO terms.

  • If no GO annotation columns are present, the function returns only the preprocessed 2d dataframe.

Details

The function executes the following:

  1. Reads the file.

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

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

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

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