Estimating Cell Type Composition from Methylation Sequencing Data


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Documentation for package ‘bisect’ version 0.9.0

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alpha_blood Recommended values for a Dirichlet prior on cell composition in blood samples. Estimated by fitting Dirichlet distribution to cell counts data.
baseline_GSE40279 Cell composition for 650 individuals from GSE40279. Estimated by running an array method on the original (array) data.
bisect_semi_suprevised Add together two numbers.
bisect_supervised Add together two numbers.
methylation_GSE40279 Simulated amount of methylated reads for 650 individuals from GSE40279. The data was sub-sampled to simulate a 30X coverage. Only 241 sites that are known to differ substaintally between cell types are recorded.
reference_blood A reference containing methylation proportions for pure cell types in the 241 chosen sites.
total_reads_GSE40279 Simulated amount of total reads reads for 650 individuals from GSE40279. The data was sub-sampled to simulate a 30X coverage. Only 241 sites that are known to differ substaintally between cell types are recorded.