API for prewas
Data Pre-Processing for Bacterial Genome-Wide Association Studies
| Global functions | |
|---|---|
| build_tree | Source code |
| check_if_binary_matrix | Source code |
| check_is_number | Source code |
| check_is_this_class | Source code |
| check_is_tree | Source code |
| check_num_overlap_genes_match_num_impact | Source code |
| check_setequal_tree_mat | Source code |
| check_snpeff_user_input | Source code |
| check_tree_is_rooted | Source code |
| clean_up_cds_name_from_gff | Source code |
| collapse_snps_into_genes | Man page Source code |
| collapse_snps_into_genes_by_impact | Man page Source code |
| dup_snps_in_overlapping_genes | Source code |
| dup_snps_in_overlapping_genes_snpeff | Source code |
| format_inputs | Source code |
| get_allele_names | Source code |
| get_ancestral_alleles | Source code |
| get_gene_mat_by_impact | Source code |
| get_gene_names | Source code |
| get_major_alleles | Source code |
| gff | Man page |
| identify_variant_sites | Source code |
| is_file | Source code |
| is_this_class | Source code |
| keep_only_variant_sites | Source code |
| load_vcf_file | Source code |
| make_all_tree_edges_positive | Source code |
| make_binary_matrix | Source code |
| outgroup | Man page |
| parse_snpeff | Source code |
| prewas | Man page Source code |
| read_gff | Source code |
| read_in_tree | Source code |
| remove_invariant_sites | Source code |
| remove_unknown_alleles | Source code |
| replace_non_ATGC_with_N | Source code |
| results | Man page |
| root_tree | Source code |
| snpeff_vcf | Man page |
| split_multi_to_biallelic_snps | Source code |
| subset_gff | Source code |
| subset_tree_and_matrix | Source code |
| tree | Man page |
| vcf | Man page |
