dot-runTukey: Fit Tukey median polish

In Vitek-Lab/MSstats: Protein Significance Analysis in DDA, SRM and DIA for Label-free or Label-based Proteomics Experiments

Fit Tukey median polish

Description

Fit Tukey median polish

Usage

.runTukey(input, is_labeled, censored_symbol, remove50missing)

Arguments

input	data.table with data for a single protein
is_labeled	logical, if TRUE, data is coming from an SRM experiment
censored_symbol	Missing values are censored or at random. 'NA' (default) assumes that all 'NA's in 'Intensity' column are censored. '0' uses zero intensities as censored intensity. In this case, NA intensities are missing at random. The output from Skyline should use '0'. Null assumes that all NA intensites are randomly missing.
remove50missing	only for summaryMethod = "TMP". TRUE removes the proteins where every run has at least 50% missing values for each peptide. FALSE is default.

Value

data.table

Vitek-Lab/MSstats documentation built on Nov. 4, 2024, 3:08 p.m.