FlowSorted.BloodExtended.450klegacy.compTable: FlowSorted.BloodExtended.450klegacy.compTable

In immunomethylomics/FlowSorted.BloodExtended.EPIC: Illumina EPIC data on extended immunomagnetic sorted blood populations

FlowSorted.BloodExtended.450klegacy.compTable

Description

This object is a matrix of dimensions 1500 by 12 consisting of the average DNA methylation values fo the probes included in the IDOL optimized CpGs per each of the twelve cell types available to use in the 450K platform. These CpGs are used as the backbone for deconvolution and were selected because their methylation signature differs across the twelve normal leukocyte subtypes.

Researchers who want to project directly their estimates with 450k data can use this matrix of different cellular populations ( neutrophils (Neu), eosinophils (Eos), basophils (Bas), monocytes (Mono),B lymphocytes naive (Bnv), B lymphocytes memory (Bmem), T helper lymphocytes naive (CD4nv), T helper lymphocytes memory (CD4mem), T regulatory cells (Treg), T cytotoxic lymphocytes naive (CD8nv), T cytotoxic lymphocytes memory (CD8mem), and natural killer lymphocytes (NK)).

Usage

FlowSorted.BloodExtended.450klegacy.compTable

Format

A class: matrix, dimensions: 1500 12 The format is: num [1:1500, 1:12] 0.95 0.886 0.769 0.672 ...

Value

numeric matrix 1500 rows 12 columns

See Also

References

1. LA Salas et al. (2021) Enhanced cell deconvolution of peripheral blood using DNA methylation for high-resolution immune profiling. (Under review)

2. LA Salas et al. (2018). An optimized library for reference-based deconvolution of whole-blood biospecimens assayed using the Illumina HumanMethylationEPIC BeadArray. Genome Biology 19, 64. doi: 10.1186/s13059-018-1448-7.

3. DC Koestler et al. (2016). Improving cell mixture deconvolution by identifying optimal DNA methylation libraries (IDOL). BMC bioinformatics. 17, 120. doi: 10.1186/s12859-016-0943-7

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

5. K Gervin, LA Salas et al. (2019) Systematic evaluation and validation of references and library selection methods for deconvolution of cord blood DNA methylation data. Clin Epigenetics 11,125. doi: 10.1186/s13148-019-0717-y

Examples

# Do not run
# data("FlowSorted.BloodExtended.450klegacy.compTable")
# head(FlowSorted.BloodExtended.450klegacy.compTable)

immunomethylomics/FlowSorted.BloodExtended.EPIC documentation built on Jan. 29, 2024, 8:43 p.m.