R: Vaccine study Data

vac18 {mixOmics} | R Documentation

## Vaccine study Data

### Description

The data come from a trial evaluating a vaccine based on HIV-1 lipopeptides in HIV-negative volunteers. The vaccine (HIV-1 LIPO-5 ANRS vaccine) contains five HIV-1 amino acid sequences coding for Gag, Pol and Nef proteins. This data set contains the expression measure of a subset of 1000 genes from purified in vitro stimulated Peripheral Blood Mononuclear Cells from 42 repeated samples (12 unique vaccinated participants) 14 weeks after vaccination, , 6 hours after in vitro stimulation by either (1) all the peptides included in the vaccine (LIPO-5), or (2) the Gag peptides included in the vaccine (GAG+) or (3) the Gag peptides not included in the vaccine (GAG-) or (4) without any stimulation (NS).

### Usage

    data(vac18)

### Format

A list containing the following components:

`gene`

  data frame with 42 rows and 1000 columns. The expression measure of 1000 genes for the 42 samples (PBMC cells from 12 unique subjects).

`stimulation`

  is a fctor of 42 elements indicating the type of in vitro simulation for each sample.

`sample`

  is a vector of 42 elements indicating the unique subjects (for example the value '1' correspond to the first patient PBMC cells). Note that the design of this study is unbalanced.

`tab.prob.gene`

  is a data frame with 1000 rows and 2 columns, indicating the Illumina probe ID and the gene name of the annotated genes.

### Details

This is a subset of the original study for illustrative purposes.

### References

Salmon-Ceron D, Durier C, Desaint C, Cuzin L, Surenaud M, Hamouda N, Lelievre J, Bonnet B, Pialoux G, Poizot-Martin I, Aboulker J, Levy Y, Launay O, trial group AV: Immunogenicity and safety of an HIV-1 lipopeptide vaccine in healthy adults: a phase 2 placebo-controlled ANRS trial. AIDS 2010, 24(14):2211-2223.

[Package mixOmics version 6.3.2 Index]