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binomial_naive_bayes()
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binomial_naive_bayes
|
|
cal_fn()
|
cal_fn
|
|
cal_fp()
|
cal_fp
|
|
cal_met_snp()
|
cal_met_snp
|
|
calculate_mcc()
|
calculate_mcc
|
|
calculate_mcc_multi()
|
calculate_mcc_multi
|
|
calculate_percent()
|
calculate_percent
|
|
calculate_simpson()
|
calculate_simpson
|
|
calculate_simpson_by_group()
|
calculate_simpson_by_group
|
|
calculate_state()
|
calculate_state
|
|
calculate_variant_within_group()
|
identify_group_variant_breakdown
|
|
check_fasta_meta_mapping()
|
check_fasta_meta_mapping
|
|
check_meta_target()
|
check_meta_target
|
|
check_multistate()
|
check_multistate
|
|
check_percent()
|
check_percent
|
|
coef(<binomial_naive_bayes>)
|
coef.binomial_naive_bayes
|
|
combine_fastq_search_result()
|
combine_fastq_search_result
|
|
combine_search_string_result()
|
combine_search_string_result
|
|
combine_search_string_result_from_files()
|
combine_search_string_result_from_files
|
|
combine_search_string_result_from_list()
|
combine_search_string_result_from_list
|
|
estimate_coverage()
|
estimate_coverage
|
|
extend_length()
|
extend_length
|
|
find_optimised_snps()
|
find_optimised_snps
|
|
full_merge()
|
full_merge
|
|
full_merge_1()
|
full_merge_1
|
|
generate_kmer_search_string()
|
generate_kmer_search_string
|
|
generate_kmers()
|
generate_kmers
|
|
generate_pattern()
|
generate_pattern
|
|
generate_prioritisation()
|
generate_prioritisation
|
|
generate_snp_search_string()
|
generate_snp_search_string
|
|
get_all_process_methods()
|
get_all_process_methods
|
|
get_binomial_tables()
|
get_binomial_tables
|
|
get_metric_fun()
|
get_metric_fun
|
|
get_snps_set()
|
get_snps_set
|
|
identify_overlaps()
|
identify_overlaps
|
|
infer_from_combined()
|
infer_from_combined
|
|
iterate_merge()
|
iterate_merge
|
|
iterate_through()
|
iterate_through
|
|
map_profile_to_target()
|
map_profile_to_target
|
|
match_count()
|
match_count
|
|
mcc_calculation()
|
mcc_calculation
|
|
merge_fasta()
|
merge_fasta
|
|
output_result()
|
output_result
|
|
output_to_files()
|
output_to_files
|
|
parse_group_mcc()
|
parse_group_mcc
|
|
parse_group_mcc_multi()
|
parse_group_mcc_multi
|
|
predict(<binomial_naive_bayes>)
|
predict.binomial_naive_bayes
|
|
predict_balk()
|
predict_balk
|
|
print(<binomial_naive_bayes>)
|
print.binomial_naive_bayes
|
|
process_allele()
|
process_allele
|
|
process_kmer_result()
|
process_kmer_result
|
|
process_result_file()
|
process_result_file
|
|
process_snp_result()
|
process_snp_result
|
|
profile_to_group_result()
|
profile_to_group_result
|
|
read_fasta()
|
read_fasta
|
|
read_sequences_from_fastq()
|
read_sequences_from_fastq
|
|
remove_snp_conflict()
|
remove_snp_conflic
|
|
resolve_IUPAC_missing()
|
resolve_IUPAC_missing
|
|
reverse_complement()
|
reverse_complement
|
|
scramble_sequence()
|
scramble_sequence
|
|
search_from_fastq_reads()
|
search_from_fastq_reads
|
|
search_from_reads()
|
search_from_reads
|
|
sequence_reads_match_count()
|
sequence_reads_match_count
|
|
summarise_result()
|
summarise_result
|
|
summary(<binomial_naive_bayes>)
|
summary.binomial_naive_bayes
|
|
train_balk()
|
train_balk
|
|
transform_snp()
|
transform_snp
|
|
translate_position()
|
translate_position
|
|
view_mcc()
|
view_mcc
|
|
view_mcc_multi()
|
view_mcc_multi
|
|
view_percent()
|
view_percent
|
|
view_simpson()
|
view_simpson
|
|
write_fasta()
|
write_fasta
|