Stratifying mutations observed in cell-free DNA and white blood cells as germline, hematopoietic, or somatic

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Documentation for package ‘plasmut’ version 1.4.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

crcseq	This data is an example dataset to show how to use the package
importance_sampler	Importance sampler to estimate marginal likelihoods and Bayes factors
model_w	Estimate the marginal likelihood that mutations in buffy coat and cfDNA reflect CH or correspond to germline mutations. If germline, the allele frequency should be 50 percent. The prior should be diffuse enough to handle CHIP mutations which are potentially way less than 50 percent
plasma_somatic	Estimate the marginal likelihood that variants identified in cell-free DNA are derived from tumor cells (ctDNA-derived)
plasmut	Bayesian models for estimating the origin of a sequenced DNA fragment
wbc_somatic	Estimate the marginal likelihood of observing somatic mutations from CTCs present in buffy coat p(y_w | theta_w, n_w, model_S) x p(theta_w| Model_S) theta_w | model_S ~ beta(1, 999) ## sequencing error or CTC