IDOLOptimizedCpGs.compTable: IDOL Optimized CpGs matrix for adult blood DNA methylation...
In immunomethylomics/FlowSorted.Blood.EPIC: Illumina EPIC data on immunomagnetic sorted peripheral adult blood cells
IDOLOptimizedCpGs.compTable R Documentation
IDOL Optimized CpGs matrix for adult blood DNA methylation deconvolution EPIC
Description
This object is a matrix of dimensions 450 x 6 consisting of the average
DNA methylation values fo the probes included in the IDOL optimized
CpGs per each of the six cell types available. These CpGs are used as
the backbone for deconvolution and were selected because their
methylation signature differs across the six normal leukocyte subtypes.
Usage
IDOLOptimizedCpGs.compTable
Format
An object of class "matrix" of dimensions 450 x 6.
The format is:
num [1:450, 1:6] 0.197 0.105 0.135 0.654 0.246 ...
References
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
DC Koestler et al. (2016). Improving cell mixture
deconvolution by identifying optimal DNA methylation libraries (IDOL).
BMC bioinformatics. 17, 120. doi:
10.1186/s13059-018-1448-7.
Examples
# data ("IDOLOptimizedCpGs.compTable")
# head(IDOLOptimizedCpGs.compTable)
# See ?estimateCellCounts2 for deconvolution examples (advanced user option)
immunomethylomics/FlowSorted.Blood.EPIC documentation built on May 24, 2023, 2:22 a.m.
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| IDOLOptimizedCpGs.compTable | R Documentation |
IDOL Optimized CpGs matrix for adult blood DNA methylation deconvolution EPIC
Description
This object is a matrix of dimensions 450 x 6 consisting of the average DNA methylation values fo the probes included in the IDOL optimized CpGs per each of the six cell types available. These CpGs are used as the backbone for deconvolution and were selected because their methylation signature differs across the six normal leukocyte subtypes.
Usage
IDOLOptimizedCpGs.compTable
Format
An object of class "matrix" of dimensions 450 x 6.
The format is: num [1:450, 1:6] 0.197 0.105 0.135 0.654 0.246 ...
References
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
DC Koestler et al. (2016). Improving cell mixture deconvolution by identifying optimal DNA methylation libraries (IDOL). BMC bioinformatics. 17, 120. doi: 10.1186/s13059-018-1448-7.
Examples
# data ("IDOLOptimizedCpGs.compTable")
# head(IDOLOptimizedCpGs.compTable)
# See ?estimateCellCounts2 for deconvolution examples (advanced user option)
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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