Man pages for surh/HMVAR
Human Microbiome Variant Analysis in R
| annotate_gos | Annotate GO terms |
| annots_to_geneGO | Convert annotation table to gene or annotation list for topGO |
| assign_allele | Assign alleles bases on allele frequency and depth |
| benchmark_imputation | Benchmark mice imputation |
| bimbam_impute | Impute genotypes with BIMBAM |
| calculate_dos | Calculate Direction of Selection |
| calculate_fst | Calculate Fixation Index (Fst) |
| calculate_mktable | Calculate McDonald-Kreitman contingency table |
| calculate_p_error | Calculate prob of error |
| calculate_prevalence | Calculate taxon prevalence |
| check_map | Process map |
| check_midas_data | Checks loaded midas data |
| check_pvals_in_file | Check p-values in MKtest.py outfile |
| check_pvalues | Check p-values |
| determine_sample_dist | Determine distributiion within sample |
| determine_snp_dist | SNP distribution between sites |
| determine_snp_effect | Determine the effect of a coding variant on the aminoacid... |
| determine_substitution_type | Determine DNA substitution type |
| dos | Calculate Direction of Selection from SNV data |
| expand_annot | Expand annotation |
| find_singletons | Find singletons |
| format_input | Formats input form HMMCP 16S files |
| format_input_hmqcp | Read HMQCP input |
| gemma_kinship | Calculate kinship matrix with GEMMA |
| gemma_lmm | Run LMM via GEMMA |
| gene_midas_data | Get all MIDAS data from a gene |
| gene_sel_fun | gene selection function |
| gene_snv_aln | Get gene SNV alignment |
| genome_wide_ni | Calculate genome-wide NI and alpha |
| get_mk_results_files | Get files for MK results |
| get_sequence_fragment | Get sequence fragment |
| get_site_dist | Determine whether a variant site is fixed or polymorphic |
| group_size | Size of groups |
| gsea | Gene-set enrichment analysis |
| match_freq_and_depth | Match freq and depth |
| mice_impute | Imputation via mice |
| midas_dos | Direction of Selection statistics on MIDAS output |
| midas_mktest | Perform McDonald-Kreitman test on MIDAS SNPs |
| midas_to_bimbam | Convert MIDAS merge output to BIMBAM input |
| mktest | McDonald-Kreitman test |
| mkvalues | Entries in McDonald-Kreitman table. |
| phylotype2rdp | Format HMMCP phylotype taxonomy for AMOR |
| phylotype2rdp2 | Phylotype to RDP version 2 |
| plotgg_manhattan | Manhattan plot with ggplot2 |
| plotgg_stacked_columns | Plot columns as stacked bars |
| pval_qqplot | p-value qqplot |
| qp_genotypes | Quasi-phased genotypes |
| read_eggnog | Read eggNOG mapper annotations |
| read_midas_abun | Read MIDAS abundance file |
| read_midas_data | Read midas snp merge data |
| read_midas_info | Read MIDAS snps_info.txt file |
| reexports | Objects exported from other packages |
| run_command | Run system command |
| select_samples_from_abun | Select samples that are present in mapping file |
| sign_test | Sign test |
| site_fst | Fixation Index (Fst) for one site |
| term_gsea | Gene-set Enrichment analysis on one term. |
| terms_enrichment | Enrichment analysis of annotation terms |
| test_go | Gene Ontology enrichment via topGO |
| test_singleton_enrichment | Test for singleton enrichments |
| tidy_mice | Tidy mice |
| variable_dist_per_site | Calculated distribution of variable per site |
| varsites_pipeline | Varsites pipeline |
| window_fst | Sliding window Fst calculation |
