estimateLC {normalize450K} | R Documentation

## Estimation of Leukocyte composition for whole blood samples

### Description

Estimate leukocyte composition from whole blood DNA methylation

### Usage

    estimateLC(eSet)

### Arguments

`eSet` | A Biobase eSet object as returned from a call of `normalize450K`

### Details

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 as described by Heiss et al. (2016) 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')`.

### Value

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

### Author(s)

Jonathan A. Heiss

### References

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

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

Heiss JA, et al. (2016). Training a model for estimating leukocyte composition using whole-blood DNA methylation and cell counts as reference. Epigenomics, doi:10.2217/epi-2016-0091

[Package normalize450K version 1.8.0 Index]