BreastEpithelialSubtypes: BreastEpithelialSubtypes

In tombartlett/BreastEpithelialSubtypes: Estimate breast tissue cell-type proportions.

BreastEpithelialSubtypes

Description

Usage:
estProps <- BreastEpithelialSubtypes(DNAmeData, RNAseqData, hierarchical=T)

Where:
'estProps' is the estimated proportions of the important cell-types of the breast.
'DNAmeData' is the DNA methylation microarray data-set of interest (with features/CpGs in rows, and samples in columns).
'RNAseqData' is the RNA-seq data-set (with features/genes in rows, and samples in columns). At least one of 'DNAmeData' and 'RNAseqData' must be provided. If both 'DNAmeData' and 'RNAseqData' are provided, their columns must correspond to the same tissue samples. 'hierarchical' determines whether to also estimate the proportions of the breast epithelial subtypes in relation to fat, adipose, and immune cells. It is only available if DNAmeData is provided.

Details

Estimates breast tissue cell-type proportions from DNA methylation microarray data, including the breast epithelium cell-subtypes luminal progenitor, mature luminal, and basal, as described in: https://www.biorxiv.org/content/10.1101/2021.05.17.444493

Author(s)

Thomas Bartlett.

References

Bartlett, T. E., Chandna, S., & Roy, S. (2021). Inference of tissue relative proportions of the breast epithelial cell types luminal progenitor, basal, and luminal mature. https://www.biorxiv.org/content/10.1101/2021.05.17.444493

Nguyen, Q. H., Pervolarakis, N., Blake, K., Ma, D., Davis, R. T., James, N., ... & Kessenbrock, K. (2018). Profiling human breast epithelial cells using single cell RNA sequencing identifies cell diversity. Nature communications, 9(1), 1-12.

Pellacani, D., Bilenky, M., Kannan, N., Heravi-Moussavi, A., Knapp, D. J., Gakkhar, S., ... & Marra, M. A. (2016). Analysis of normal human mammary epigenomes reveals cell-specific active enhancer states and associated transcription factor networks. Cell reports, 17(8), 2060-2074.

The results published here are in whole or part based upon data generated by The Canadian Epigenetics, Epigenomics, Environment and Health Research Consortium (CEEHRC) initiative funded by the Canadian Institutes of Health Research (CIHR), Genome BC, and Genome Quebec. Information about CEEHRC and the participating investigators and institutions can be found at http://www.cihr-irsc.gc.ca/e/43734.html

tombartlett/BreastEpithelialSubtypes documentation built on July 8, 2022, 8:11 a.m.