The HiBED package contains reference libraries derived from Illumina HumanMethylation450K and Illumina HumanMethylationEPIC DNA methylation microarrays (Zhang Z, Salas LA et al. 2023), consisting of 6 astrocyte, 12 endothelial, 5 GABAergic neuron, 5 glutamatergic neuron, 18 microglial, 20 oligodendrocyte, and 5 stromal samples from public resources.
The reference libraries were used to estimate proportions of 7 major brain cell types in 450K and EPIC bulk brain samples using a modified version of the algorithm constrained projection/quadratic programming described in Houseman et al. 2012.
Loading package:
Objects included:
1. HiBED_Libraries contains 4 libraries for deconvolution
We offer the function HiBED_deconvolution to estimate proportions for 7 major brain cell types, including GABAergic neurons, glutamatergic neurons, astrocytes, microglial cells, oligodendrocytes, endothelial cells, and stromal cells. The estimates are calculated using modified CP/QP method described in Houseman et al. 2012.
see ?HiBED_deconvolution for details
# Step 1 load and process example
library(FlowSorted.Blood.EPIC)
library(FlowSorted.DLPFC.450k)
library(minfi)
Mset<-preprocessRaw(FlowSorted.DLPFC.450k)
Examples_Betas<-getBeta(Mset)
# Step 2: use the HiBED_deconvolution function in combinatation with the
# reference libraries for brain cell deconvolution.
HiBED_result<-HiBED_deconvolution(Examples_Betas, h=2)
head(HiBED_result)
#> Endothelial Stromal Astrocyte Microglial Oligodendrocyte GABA
#> 813_N NaN NaN 0.8548534 0.7915309 5.643616 14.867764
#> 1740_N NaN NaN 0.8524800 1.1596800 3.747840 17.805161
#> 1740_G 4.2758290 2.0241710 6.3462006 19.9935161 60.030283 3.336364
#> 1228_G 2.6479470 2.1120530 4.2803944 7.2064838 78.253122 2.508475
#> 813_G 2.5763484 1.9536516 5.4130230 14.4480688 69.668908 2.738889
#> 1228_N 0.5389908 0.7110092 1.5104187 1.6272037 7.832378 14.880146
#> GLU
#> 813_N 70.812236
#> 1740_N 70.134839
#> 1740_G 4.003636
#> 1228_G 2.991525
#> 813_G 3.211111
#> 1228_N 69.869854sessionInfo()
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minfi Tools to analyze & visualize Illumina Infinium methylation arrays.