Run estimateLC.R
estimateLC(meth, ref, constrained = FALSE)Matrix of beta values
Choice of reference dataset: available options are saliva and salivaEPIC. The functions are extracted from ewastools (Murat, K, et al. 2020) and adapted to work onloy with the saliva reference panel of Middleton et al. 2020.
Force that all cell proportions sum up to 1.
A data.table containing estimated cell proportions for each sample.
Murat K, et al. Ewastools: Infinium Human Methylation BeadChip pipeline for population epigenetics integrated into Galaxy. GigaScience. 2020;9(5):giaa049. Houseman EA, Accomando WP, Koestler DC, et al. DNA methylation arrays as surrogate measures of cell mixture distribution. BMC Bioinformatics. 2012;13:86. Reinius LE, Acevedo N, Joerink M, et al. Differential DNA methylation in purified human blood cells: implications for cell lineage and studies on disease susceptibility. PLoS One. 2012;7(7):e41361. Bakulski KM, Feinberg JI, Andrews SV, et al. DNA methylation of cord blood cell types: applications for mixed cell birth studies. Epigenetics. 2016;11(5):354-362. de Goede OM, Razzaghian HR, Price EM, et al. Nucleated red blood cells impact DNA methylation and expression analyses of cord blood hematopoietic cells. Clinical Epigenetics. 2015;7:95. Gervin K, Salas LA, Bakulski KM, 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;11(9):690-698. Gervin K, Salas LA, Bakulski KM, et al. Systematic evaluation and validation of reference and library selection methods for deconvolution of cord blood DNA methylation data. bioRxiv. 2019. doi:10.1101/570457. Salas LA, Koestler DC, Butler RA, et al. An optimized library for reference-based deconvolution of whole-blood biospecimens assayed using the Illumina HumanMethylationEPIC BeadArray. Genome Biology. 2018;19:64. Heiss JA, Just AC, Brenner H. Training a model for estimating leukocyte composition using whole-blood DNA methylation and cell counts as reference. Epigenomics. 2017;9(1):13-20. Middleton LYM, Dou J, Mill J, et al. Saliva cell type DNA methylation reference panel for epidemiology studies in children. 2020.
tmp <- tempdir()
stopifnot(dir.exists(tmp))
if (FALSE) { # \dontrun{
estimateLC(
meth = beta,
ref = "saliva",
constrained = FALSE
)
} # }