estimateLC: Estimation of Leukocyte composition for whole blood samples

Description

[Experimental] Estimate leukocyte composition from whole blood DNA methylation

Usage

estimateLC(eSet)

Arguments

eSet

A Biobase eSet object as returned from a call of normalize450K

Value

Returns the eSet object with cell proportions estimates added to the phenoData slot.

Details

This is an experimental feature. Cell proportions are estimated using the algorithm developed by Houseman et al. (2012) by two different models. The first model was trained on a dataset of purified leukocytes (Reinius et al., 2012) and provides predictions for six cell types (granulocytes, monocytes, CD8+ T cells, CD4+ T cells, natural killer cells and CD19+ B cells), the second model was trained on whole blood samples from the LOLIPOP study and provides predictions for 4 cell types (neutrophils, eosinophils, lymphocytes, monocytes -- ignore the prediction for basophils). Use this function only for normalized data (with normalize450K(...,tissue='Blood').

References

Houseman, Eugene Andres, et al. DNA methylation arrays as surrogate measures of cell mixture distribution. BMC bioinformatics 13.1 (2012): 1. doi:10.1186/1471-2105-13-86

Reinius, Lovisa E., et al. Differential DNA methylation in purified human blood cells: implications for cell lineage and studies on disease susceptibility. PloS one 7.7 (2012): e41361. doi:10.1371/journal.pone.0041361