MSstatsBalancedDesign: Creates balanced design by removing overlapping fractions and...

In Vitek-Lab/MSstatsConvert: Import Data from Various Mass Spectrometry Signal Processing Tools to MSstats Format

Creates balanced design by removing overlapping fractions and filling incomplete rows

Description

Creates balanced design by removing overlapping fractions and filling incomplete rows

Usage

MSstatsBalancedDesign(
  input,
  feature_columns,
  fill_incomplete = TRUE,
  handle_fractions = TRUE,
  fix_missing = NULL,
  remove_few = TRUE
)

Arguments

input	data.table processed by the MSstatsPreprocess function
feature_columns	str, names of columns that define spectral features
fill_incomplete	if TRUE (default), ensures that rows with missing data for specific features are added as NA. For example, if the y10 ion of peptideA is measured in the "disease" samples but entirely missing for the "healthy" samples, rows with NA values will be created for the y10 ion of peptideA in the "healthy" group. This process increases the number of rows to account for all possible feature-sample combinations.
handle_fractions	if TRUE (default), overlapping fractions will be resolved
fix_missing	str, optional. Defaults to NULL, which means no action. If not NULL, must be one of the options: "zero_to_na" or "na_to_zero". If "zero_to_na", Intensity values equal exactly to 0 will be converted to NA. If "na_to_zero", missing values will be replaced by zeros.
remove_few	lgl, if TRUE, features with one or two measurements across runs will be removed.

Value

data.frame of class MSstatsValidated

Examples

unbalanced_data = system.file("tinytest/raw_data/unbalanced_data.csv", 
                              package = "MSstatsConvert")
unbalanced_data = data.table::as.data.table(read.csv(unbalanced_data))
balanced = MSstatsBalancedDesign(unbalanced_data, 
                                 c("PeptideSequence", "PrecursorCharge",
                                   "FragmentIon", "ProductCharge"))
dim(balanced) # Now balanced has additional rows (with Intensity = NA)
# for runs that were not included in the unbalanced_data table

Vitek-Lab/MSstatsConvert documentation built on Jan. 22, 2025, 4:27 a.m.