Represents Kmers As Integers Along The Genome

base2kmer | Converts a base representation (base 4 default) to the kmer |

base5to10 | Converts a base representation (base 4 default) to normal... |

base5to10_c | Converts a base representation (base 4 default) to normal... |

build_alphabet | Sets up the alphabet for indexing nucleotides |

convert10to5 | Converts a normal (base 10) integer to base representation... |

convert10to5_c | Converts a normal (base 10) integer to base representation... |

convert10tobase_c | Converts a normal (base 10) integer to base representation... |

convert10tokmer | Converts a normal (base 10) integer to the equivalent kmer |

dna_input | Part of a DNA sequence |

kmer2base | Converts a kmer to a number in base 4 (default) |

kmer_counter | Represents the kmers present in the input with their integer... |

kmer_counter_c | Represents the kmers present in the input with their integer... |

kmer_counter_para_c | Represents the kmers present in the input with their integer... |

kmer_counter_wrapper | Represents the kmers present in the input with their integer... |

kmer_counter_wrapper_c | Represents the kmers present in the input with their integer... |

kmer_dot_prod | Computes the dot product of the parameters with the kmer... |

kmer_dot_prod_c | Computes the dot product of the parameters with the kmer... |

kmermods | 'kmermods': Represents Kmers As Integers Along The Genome |

kmerto10 | Converts a kmer to it's normal (base 10) integer... |

l1_prox_op | L1 regulatisation proximal operator |

let2base | Finds the integer that represents the nucleotide |

let2base_c | Finds the integer that represents the nucleotide |

loglik_linesearch | Calculates the log likelihood of the data, given some... |

loglik_logreg | Calculates the log likelihood of the data, given some... |

loglik_log_reg_grad | Computes the gradient of the log likelihood of a logistic... |

log_reg_wrapper | Computes the gradient of the log likelihood of a logistic... |

lower_kmer | Finds the (k-1)mer integer representation ffrom the kmer... |

mismatch_kmers | Counts the number of mismatches between two kmers, when... |

params_peaks_noslide | Computes the vector with which to update the parameters in a... |

params_peaks_noslide_w_error | Computes the vector with which to update the parameters in a... |

predict_peaks | Computes the predictions for the logistic regression |

rev_comp | Finds the reverse complementary kmer, in integer form,... |

rev_comp_c | Finds the reverse complementary kmer, in integer form,... |

rev_comp_meth | Finds the reverse complementary kmer, in integer form, using... |

total_error | Computes the total error of the predictions. |

unwrap_kmers | Takes a longer kmer and converts it into a vector of its... |

unwrap_kmers_vect | Takes in a single long kmer, for example a 26mer, and returns... |

update_paras | Creates the update for the parameter vector according to the... |

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