cell_composition: Cell composition

estimateLCR Documentation

Cell composition

Description

Estimation of cell proportions for blood and saliva using the Houseman algorithm

Usage

estimateLC(meth, ref, constrained = FALSE)

Arguments

meth

Matrix of beta values

ref

Choice of reference dataset: available options are 'HRS' (Health and Retirement Study), 'Reinius' [2]', Bakulski' [3], 'deGoede' [4], 'Gervin'[5], 'Lin' [6], 'Mill' [GSE103541], 'Salas' [7], 'Lolipop' [8] or combinations of them, concatenated by '+', e.g. 'Reinius+Lin' (you might have to flip first and second name)). Furthermore, the option 'saliva' and 'salivaEPIC' are available [9].

constrained

Force that all cell proportions sum up to 1.

Value

Estimated cell proportions B-lymphocytes, CD4 T-cells, CD8 T-cells, granulocytes, monocytes, natural killer cells (and nucleated red blood cells) using the Houseman algorithm [1]. Models were trained on various reference datasets of purified cell types.

References

Houseman EA, et al. DNA methylation arrays as surrogate measures of cell mixture distribution. BMC bioinformatics. 2012 Dec 1;13(1):86.

Reinius LE, et al. Differential DNA methylation in purified human blood cells: implications for cell lineage and studies on disease susceptibility. PloS one. 2012 Jul 25;7(7):e41361.

Bakulski KM, et al. DNA methylation of cord blood cell types: applications for mixed cell birth studies. Epigenetics. 2016 May 3;11(5):354-62.

de Goede OM, et al. Nucleated red blood cells impact DNA methylation and expression analyses of cord blood hematopoietic cells. Clinical epigenetics. 2015 Dec;7(1):95.

Gervin K, et al. Cell type specific DNA methylation in cord blood: A 450K-reference data set and cell count-based validation of estimated cell type composition. Epigenetics. 2016 Sep 1;11(9):690-8

Gervin K, et al. Systematic evaluation and validation of reference and library selection methods for deconvolution of cord blood DNA methylation data. bioRxiv. 2019 March; DOI:10.1101/570457

Salas LA, et al. An optimized library for reference-based deconvolution of whole-blood biospecimens assayed using the Illumina HumanMethylationEPIC BeadArray. Genome biology. 2018 Dec;19(1):64.

Heiss JA, et al. Training a model for estimating leukocyte composition using whole-blood DNA methylation and cell counts as reference. Epigenomics. 2017 Jan;9(1):13-20.

Middleton LYM, et al. Saliva cell type DNA methylation reference panel for epidemiology studies in children. 2020 Sep;


hhhh5/ewastools_releases documentation built on Feb. 7, 2024, 2:57 a.m.