From 267b2bf00909bd00d4a57ba013637333b765c2b3 Mon Sep 17 00:00:00 2001 From: "Documenter.jl" Date: Sat, 30 Nov 2024 12:33:19 +0000 Subject: [PATCH] build based on 77b352e --- dev/.documenter-siteinfo.json | 2 +- dev/api/index.html | 2 +- dev/index.html | 2 +- dev/objects.inv | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/dev/.documenter-siteinfo.json b/dev/.documenter-siteinfo.json index 6e23d94..374debd 100644 --- a/dev/.documenter-siteinfo.json +++ b/dev/.documenter-siteinfo.json @@ -1 +1 @@ -{"documenter":{"julia_version":"1.11.1","generation_timestamp":"2024-11-28T10:47:25","documenter_version":"1.8.0"}} \ No newline at end of file +{"documenter":{"julia_version":"1.11.1","generation_timestamp":"2024-11-30T12:33:15","documenter_version":"1.8.0"}} \ No newline at end of file diff --git a/dev/api/index.html b/dev/api/index.html index 001967b..5c88bfa 100644 --- a/dev/api/index.html +++ b/dev/api/index.html @@ -1,2 +1,2 @@ -API · CHMMera.jl
GitHub

API Reference

CHMMera.get_chimera_probabilities — Method
get_chimera_probabilities(queries::Vector{String}, references::Vector{String}, bw::Bool = true, mutation_probabilities::Vector{Float64} = [0.0047, 0.01, 0.05, 0.1, 0.15, 0.2], base_mutation_probability::Float64 = 0.05, prior_probability::Float64 = 0.02

Compute the probability of a sequence being chimeric for each query sequence given a list of reference sequences.

Arguments

  • queries::Vector{String}: A vector of query sequences.
  • references::Vector{String}: A vector of reference sequences.
  • bw::Bool = true: A boolean indicating whether to use the Baum-Welch or the Discretized Bayesian approach.
  • mutation_probabilities::Vector{Float64} = [0.0047, 0.01, 0.05, 0.1, 0.15, 0.2]: A vector of mutation probabilities.
  • base_mutation_probability::Float64 = 0.05: The base mutation probability. Used as starting point for Baum-Welch.
  • prior_probability::Float64 = 0.02: The prior probability of a sequence being chimeric.
source
CHMMera.get_recombination_events — Method
get_recombination_events(queries::Vector{String}, references::Vector{String}, bw::Bool = true, mutation_probabilities::Vector{Float64} = [0.0047, 0.01, 0.05, 0.1, 0.15, 0.2], base_mutation_probability::Float64 = 0.05, prior_probability::Float64 = 0.02, detailed::Bool = false)

Compute the recombination events for a query sequence given a set of reference sequences.

The return type is a vector of RecombinationEvents (plural because one query can have multiple recombination events). In RecombinationEvents, recombinations is a vector of RecombinationEvents, each of which contains position, left, right, left_state, and right_state (Since FullHMMs have multiple states per reference). startingpoint is the starting point of viterbi path, pathevaluation is the probability of the second most probable reference, and logsiteprobabilities is the log probability of being at each site in the query sequence (forward * backward). If the argument detailed is false, only recombinations is computed.

Arguments

  • queries::Vector{String}: A vector of query sequences.
  • references::Vector{String}: A vector of reference sequences.
  • bw::Bool = true: A boolean indicating whether to use the Baum-Welch or the Discretized Bayesian approach.
  • mutation_probabilities::Vector{Float64} = [0.0047, 0.01, 0.05, 0.1, 0.15, 0.2]: A vector of mutation probabilities.
  • base_mutation_probability::Float64 = 0.05: The base mutation probability. Used as starting point for Baum-Welch.
  • prior_probability::Float64 = 0.02: The prior probability of a sequence being chimeric.
  • detailed::Bool = false: A boolean indicating whether to calculate pathevaluation and logsiteprobabilities.
source
+API · CHMMera.jl
GitHub

API Reference

CHMMera.get_chimera_probabilities — Method
get_chimera_probabilities(queries::Vector{String}, references::Vector{String}, bw::Bool = true, mutation_probabilities::Vector{Float64} = [0.0047, 0.01, 0.05, 0.1, 0.15, 0.2], base_mutation_probability::Float64 = 0.05, prior_probability::Float64 = 0.02

Compute the probability of a sequence being chimeric for each query sequence given a list of reference sequences.

Arguments

  • queries::Vector{String}: A vector of query sequences.
  • references::Vector{String}: A vector of reference sequences.
  • bw::Bool = true: A boolean indicating whether to use the Baum-Welch or the Discretized Bayesian approach.
  • mutation_probabilities::Vector{Float64} = [0.0047, 0.01, 0.05, 0.1, 0.15, 0.2]: A vector of mutation probabilities.
  • base_mutation_probability::Float64 = 0.05: The base mutation probability. Used as starting point for Baum-Welch.
  • prior_probability::Float64 = 0.02: The prior probability of a sequence being chimeric.
source
CHMMera.get_recombination_events — Method
get_recombination_events(queries::Vector{String}, references::Vector{String}, bw::Bool = true, mutation_probabilities::Vector{Float64} = [0.0047, 0.01, 0.05, 0.1, 0.15, 0.2], base_mutation_probability::Float64 = 0.05, prior_probability::Float64 = 0.02, detailed::Bool = false)

Compute the recombination events for a query sequence given a set of reference sequences.

The return type is a vector of RecombinationEvents (plural because one query can have multiple recombination events). In RecombinationEvents, recombinations is a vector of RecombinationEvents, each of which contains position, left, right, left_state, and right_state (Since FullHMMs have multiple states per reference). startingpoint is the starting point of viterbi path, pathevaluation is the probability of the second most probable reference, and logsiteprobabilities is the log probability of being at each site in the query sequence (forward * backward). If the argument detailed is false, only recombinations is computed.

Arguments

  • queries::Vector{String}: A vector of query sequences.
  • references::Vector{String}: A vector of reference sequences.
  • bw::Bool = true: A boolean indicating whether to use the Baum-Welch or the Discretized Bayesian approach.
  • mutation_probabilities::Vector{Float64} = [0.0047, 0.01, 0.05, 0.1, 0.15, 0.2]: A vector of mutation probabilities.
  • base_mutation_probability::Float64 = 0.05: The base mutation probability. Used as starting point for Baum-Welch.
  • prior_probability::Float64 = 0.02: The prior probability of a sequence being chimeric.
  • detailed::Bool = false: A boolean indicating whether to calculate pathevaluation and logsiteprobabilities.
source
diff --git a/dev/index.html b/dev/index.html index 808374b..3ae96b8 100644 --- a/dev/index.html +++ b/dev/index.html @@ -18,4 +18,4 @@ julia> get_recombination_events(queries, refs; detailed = true) 2-element Vector{DetailedRecombinationEvents}: (recombinations = RecombinationEvent[(position = 7, left = 1, right = 2, left_state = 1, right_state = 2)], startingpoint = 1, pathevaluation = 0.995612088796054, logsiteprobabilities = [-0.007751384549707252, -0.006081763823303499, -0.00439756634058619, -0.00464963436088528, -0.01670468631375581, -0.7003603824992484, -4.360877076008885, -0.0003315532714940339, -1.1770957131840287e-5, -4.643262233303136e-6, -4.698595592046717e-5, -0.0017033680895343628]) - (recombinations = RecombinationEvent[], startingpoint = 2, pathevaluation = -Inf, logsiteprobabilities = Float64[]) + (recombinations = RecombinationEvent[], startingpoint = 2, pathevaluation = -Inf, logsiteprobabilities = Float64[]) diff --git a/dev/objects.inv b/dev/objects.inv index 3bd44ae..789ccbf 100644 --- a/dev/objects.inv +++ b/dev/objects.inv @@ -1,6 +1,6 @@ # Sphinx inventory version 2 # Project: CHMMera.jl -# Version: 0.1.0 +# Version: 0.1.1 # The remainder of this file is compressed using zlib. xMk@6nkQiiklƑnج w׏JxecIϻU$^Ɋ|( # #̠ݖ#=/eYiE->vi4x\qr6kZLAByVޱ)^\wK8Uadwq?TvPH֤h`M_^Qxwn \ No newline at end of file