MSstatsSampleSize: MSstatsSampleSize: A package for optimal design of...

In Vitek-Lab/MSstatsSampleSize: Simulation tool for optimal design of high-dimensional MS-based proteomics experiment

Description

A set of functions for sample size calculation. The packages estimates the variance in the input protein abundance data and simulates data with pre-defined number of biological replicates based on the variance estimation. It reports the mean predictive accuracy of the classifier and mean protein importance over multiple iterations of the simulation.

functions

• estimateVar : estimate the mean abundance and variance of each protein in each condition.

• meanSDplot : draw the plot for the mean protein abundance vs standard deviation in each condition.

• simulateDataset : simulate datasets with the pre-defined size based on the preliminary data.

• designSampleSizeClassification : estimate the mean predictive accuracy and protein importance over all the simulated datasets.

• designSampleSizePCAplot : make PCA plots with the first two components for each simulated dataset.

• designSampleSizeClassificationPlots : visualization for sample size calculation in classification.

• designSampleSizeHypothesisTestingPlot : Sample size calculation plot for hypothesis testing.

Vitek-Lab/MSstatsSampleSize documentation built on Aug. 28, 2020, 10:39 a.m.