clj-deconstruct-sigs.core — clj-deconstruct-sigs 0.2.0

signature->vector clj/s

(signature->vector data)

Converts a frequencies map into a 96 element vector representing the substitution patterns.

square clj

(square x)

which-signatures clj/s

(which-signatures sample-tumor signature-set)

(which-signatures sample-tumor
                  signature-set
                  {:keys [signature-cutoff error-threshold]
                   :or {signature-cutoff 0.06 error-threshold 0.001}})

Finds a linear mixture of signature-set which best describes the given vector sample-tumor.

Accepts the following options: :signature-cutoff - A threshold for cutting weights off. Defaults to 0.06. :error-threshold - Target error reduction rate to stop optimization. Defaults to 1e-3.

Returns a map with the following keys: :seed-idx - Index of the signature that was used as the initial seed. :weights - A map of weight indices to weight. :weights* with zero contribution entries. :weights* - A map of non-zero weight indices to weight. Note that entries that have zero contribution will be missing. :product - matrix product of :weights and the provided signatures. :unknown - 1 minus the sum of weights. :diff - Element wise difference of the provided sample tumor and the product. :error-sum - Square root of the sum of the element wise square of :diff. Indicates how close the :product is from the original input.