FlowSorted.Blood.EPIC

DOI: 10.18129/B9.bioc.FlowSorted.Blood.EPIC    

This is the development version of FlowSorted.Blood.EPIC; to use it, please install the devel version of Bioconductor.

Illumina EPIC data on immunomagnetic sorted peripheral adult blood cells

Bioconductor version: Development (3.8)

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.

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)

Maintainer: Lucas A. Salas <lucas.a.salas.diaz at dartmouth.edu>

Citation (from within R, enter citation("FlowSorted.Blood.EPIC")):

Installation

To install this package, start R and enter:

if (!requireNamespace("BiocManager", quietly=TRUE))
    install.packages("BiocManager")
BiocManager::install("FlowSorted.Blood.EPIC", version = "devel")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("FlowSorted.Blood.EPIC")

 

HTML R Script FlowSorted.Blood.EPIC
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Details

biocViews ExperimentData, Genome, Homo_sapiens_Data, MethylationArrayData, MicroarrayData, Tissue, TissueMicroarrayData
Version 0.99.36
License GPL-3
Depends R (>= 3.5), minfi(>= 1.21.2), SummarizedExperiment, genefilter, quadprog, nlme, S4Vectors, graphics, stats, utils, IlluminaHumanMethylationEPICanno.ilm10b4.hg19, ExperimentHub
Imports
LinkingTo
Suggests knitr, rmarkdown, EpiDISH, FlowSorted.Blood.450k(>= 1.0.1), FlowSorted.CordBlood.450k, FlowSorted.CordBloodNorway.450k, testthat, IlluminaHumanMethylation450kmanifest(>= 0.2.0), IlluminaHumanMethylation450kanno.ilmn12.hg19(>= 0.2.1), IlluminaHumanMethylationEPICanno.ilm10b2.hg19
SystemRequirements
Enhances
URL https://github.com/immunomethylomics/FlowSorted.Blood.EPIC
BugReports https://github.com/immunomethylomics/FlowSorted.Blood.EPIC/issues.
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package FlowSorted.Blood.EPIC_0.99.36.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan)
Source Repository git clone https://git.bioconductor.org/packages/FlowSorted.Blood.EPIC
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/FlowSorted.Blood.EPIC
Package Short Url http://bioconductor.org/packages/FlowSorted.Blood.EPIC/
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