FlowSorted.Blood.EPIC

Illumina EPIC data on immunomagnetic sorted peripheral adult blood cells

Bioconductor version: 3.23 · Package version: 2.16.0

Raw data objects to be used for blood cell proportion estimation in minfi and similar packages. The FlowSorted.Blood.EPIC object is based in samples assayed by Brock Christensen and colleagues; for details see Salas et al. 2018. https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE110554.

Installation

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("FlowSorted.Blood.EPIC")

Details

Maintainer	Lucas A. Salas <lucas.a.salas.diaz@dartmouth.edu>
Author	Lucas A. Salas [cre, aut], Devin C. Koestler [aut], Rondi A. Butler [ctb], Helen M. Hansen [ctb], John K. Wiencke [ctb], Karl T. Kelsey [ctb], Brock C. Christensen [ctb], Kasper Daniel Hansen [ctb] (author and maintainer of the original minfi estimateCellCounts and internal functions), Jean-Philippe Fortin [ctb] (contributor in the original minfi estimateCellCounts and internal functions), Shan V. Andrews [ctb] (contributor in the original minfi estimateCellCounts and internal functions), E. Andres Houseman [ctb] (author of the original quadratic programming function used for cell projection), Andrew E Jaffe [ctb] (author of the original estimateCellCounts and internal functions within minfi)
License	GPL-3
URL	https://github.com/immunomethylomics/FlowSorted.Blood.EPIC
Bug Reports	https://github.com/immunomethylomics/FlowSorted.Blood.EPIC/issues.
Downloads rank	400
Source branch	RELEASE_3_23
biocViews	ExperimentData, Genome, Homo_sapiens_Data, MethylationArrayData, MicroarrayData, Tissue, TissueMicroarrayData

Download

Source package

Dependencies

Depends: R (>= 3.5), minfi(>= 1.21.2), ExperimentHub

Imports: genefilter, nlme, quadprog, graphics, stats, utils, AnnotationHub, SummarizedExperiment, S4Vectors

Suggests: knitr, rmarkdown, FlowSorted.CordBlood.450k, FlowSorted.Blood.450k(>= 1.0.1), EpiDISH, FlowSorted.CordBloodNorway.450k, testthat, IlluminaHumanMethylation450kmanifest(>= 0.2.0), IlluminaHumanMethylationEPICmanifest, IlluminaHumanMethylation450kanno.ilmn12.hg19(>= 0.2.1), IlluminaHumanMethylationEPICanno.ilm10b4.hg19

Enhances: FlowSorted.CordBloodCombined.450k(>= 1.11.5)

Reverse dependencies

Imports Me (1): HiBED

Suggests Me (3): DMRcate, FlowSorted.CordBloodCombined.450k, wateRmelon