Loading and reformatting of metabolomics data — preprocess • metastat

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

Usage

preprocess(
  fileName,
  dataSet = NULL,
  attrnames = c("gender", "treatment", "replicate"),
  zeroNA = TRUE
)

Arguments

fileName: The name of the .csv file containing metabolomics data (including the path to the file, if needed).
dataSet: The raw data set, if already loaded in R.
attrnames: A vector of strings (default = c("gender", "treatment", "replicate")) specifying the names of the attribute columns.
zeroNA: A boolean (default = TRUE) specifying whether 0's should be converted to NA's.

Value

A 2d dataframe.

Details

The function executes the following:

Reads the file.
Provides summary statistics and a histogram of all values reported in the data set.
Re-formats the data to present individual compounds as columns.
Stores the data as a data.frame and prints the levels of attributes to the user.