get_Mariathasan2018_PDL1_treatment: Get the Mariathasan2018 PD-L1 treatment data

In olapuentesantana/easierData: easier internal data and exemplary dataset from IMvigor210CoreBiologies package

Description

Obtain the gene expression data (count and tpm values) and the sample metadata from Mariathasan et al. (2018).

Usage

get_Mariathasan2018_PDL1_treatment()

Details

The SummarizedExperiment object returned contains:

• two assays: counts and tpm.

• additional sample metadata in the colData slot, including pat_id (the id of the patient in the original study), BOR to PD-L1 treatment, and TMB (Tumor Mutational Burden).

Value

A SummarizedExperiment object with counts and TPM quantifications.

Source

IMvigor210CoreBiologies package under the CC-BY license. http://research-pub.gene.com/IMvigor210CoreBiologies/

References

Óscar Lapuente-Santana, Maisa van Genderen, Peter A. J. Hilbers, Francesca Finotello, and Federica Eduati. 2021. Interpretable Systems Biomarkers Predict Response to Immune-Checkpoint Inhibitors. Patterns, 100293. https://doi.org/10.1016/j.patter.2021.100293.

Mariathasan, S., Turley, S., Nickles, D. et al. TGFB attenuates tumour response to PD-L1 blockade by contributing to exclusion of T cells. Nature 554, 544–548 (2018). https://doi.org/10.1038/nature25501.

Examples

if (interactive()) {
    se_mariathasan <- get_Mariathasan2018_PDL1_treatment()
}

olapuentesantana/easierData documentation built on Dec. 22, 2021, 4:19 a.m.