README.md

In jbp7/TEAM: Multiple Hypothesis Testing on an Aggregation Tree Method

TEAM

The R package TEAM and source file TEAM2D.R identify local 1D (one marker) and 2D regions (two markers), respectively, that differ between case and control distributions.

TEAM accompanies the paper:

Pura J., Chan C., Xie J. 2019. Multiple Testing Embedded in an Aggregation Tree to Identify 
where Two Distributions Differ. https://arxiv.org/abs/1906.07757

Installation

You can install TEAM from CRAN with:

install.packages("TEAM")

Please see the TEAM reference guide in CRAN for details.

TEAM2D.R takes in two dataframes from case (df1) and control (df0). Each dataframe contains two columns, one for each marker. The user inputs the number of breaks, m, to be created in each direction, as well as the FDR level, alpha, and number of layers, L. To use TEAM2D.R simply source the file in the working environment.

The Simulation folder contains the code to reproduce the simulations in the paper above.

The EQAPOL folder contains the code to reproduce the data analysis on the 11 individuals, as mentioned in the paper above. The case (CMV pp65) and control (Costim) flow cytometry samples for the 11 individuals can be accessed via https://dataverse.harvard.edu/dataset.xhtml?persistentId=doi:10.7910/DVN/D141FU.

jbp7/TEAM documentation built on Nov. 4, 2019, 2:22 p.m.