# Resolution-Optimised SNPs Searcher

## Documentation for package ‘minSNPs’ version 0.2.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

binomial_naive_bayes | 'binomial_naive_bayes'
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'
cal_fn | 'cal_fn'
cal_fp | 'cal_fp'
cal_met_snp | 'cal_met_snp'
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_kmers | 'generate_kmers'
generate_kmer_search_string | 'generate_kmer_search_string'
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'