BeadSorted.Saliva.EPIC: DNA Methylation RGChannelSet

In bakulskilab/BeadSorted.Saliva.EPIC: Illumina EPIC data on BeadSorted child saliva cells

DNA Methylation RGChannelSet

Description

Illumina Human Methylation data from EPIC on cell-sorted child saliva cell populations. The BeadSorted.Saliva.EPIC package contains Illumina HumanMethylationEPIC (“EPIC”)) DNA methylation microarray data from Middleton and colleagues, consisting of 38 magnetic bead sorted saliva cell references from 22 samples, formatted as an RGChannelSet object for easy integretion with other bioconductor packages.

This package contains data similar to other data packages for cell-type deconvolution, such as FlowSorted.Blood.450k and FlowSorted.Blood.EPIC. However, this package provides novel data from saliva biosamples.

Researchers may find this package useful as these samples represent cell populations (immune and epithelial cells) from cell-sorted saliva.

Implementation of cell-type estimation using these data can be performed using the ewastools package's function estimateLC.

Format

An RGChannelSet, dimensions: 1051815 60

Source

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE147318 The BeadSorted.Saliva.EPIC object is based on samples assayed by Lauren Middleton et a. (2021).

See Also

References

1. Lauren Y. M. Middleton, John Dou, Jonah Fisher, Jonathan A. Heiss, Vy K. Nguyen, Allan C. Just, Jessica Faul, Erin B. Ware, Colter Mitchell, Justin A. Colacino & Kelly M. Bakulski (2021) Saliva cell type DNA methylation reference panel for epidemiological studies in children , Epigenetics, DOI: 10.1080/15592294.2021.1890874

2. EA Houseman et al. (2012) DNA methylation arrays as surrogate measures of cell mixture distribution. BMC Bioinformatics 13, 86. doi:10.1186/1471-2105-13-86.

3. ewastools package with implementation for estimating cell type proportions in saliva using these data

https://github.com/hhhh5/ewastools

Examples

library(ExperimentHub)
query(ExperimentHub(), "BeadSorted.Saliva.EPIC")

BeadSorted.Saliva.EPIC <- ExperimentHub()[["EH4539"]]
BeadSorted.Saliva.EPIC

bakulskilab/BeadSorted.Saliva.EPIC documentation built on March 6, 2023, 9:27 a.m.