Man pages for vmikk/metagMisc
Miscellaneous functions for metagenomic analysis
| abbreviate_taxa_names | Abbreviate taxa names |
| add_metadata | Add metadata to data.frame |
| adonis_pairwise | Pairwise comparisons for permutational multivariate analysis... |
| blast_to_wide | Convert BLAST results to a wide table |
| bubble_plot | Bubble plot |
| check_tax_uniqueness | Check taxonomy uniqueness. |
| dada_learn_errors_subset | DADA2 learning the error rates based on a subset of data |
| dada_to_fasta | Write DADA sequences to fasta. |
| dfRowName | Transfer rownames of data frame to a new column (for data... |
| dissimilarity_to_distance | Transform (non-metric) dissimilarity matrix to a weighted... |
| dissimilarity_to_distance_importance_plot | Display species importance plot based on a weighted Euclidean... |
| dist2list | Convert distance matrix to data frame |
| eig_perc | Estimate the proportion of explained variance from the... |
| extract_in_parentheses | Extract information inside the parentheses from a character... |
| get_max_taxonomic_rank | Determine the lowest level of taxonomic classification |
| get_max_taxonomic_rank_DT | Determine the lowest level of taxonomic classification |
| leading_zero | Add or remove leading zeros |
| make_utax_taxonomy | Prepare taxonomy annotations in SINTAX or UTAX style. |
| make_utax_taxonomy_batch | Prepare taxonomy annotations in SINTAX or UTAX style for... |
| metagenome_contributions | Partition metagenome functional contributions according to... |
| mult_dissim | Compute beta diversity for each rarefaction iteration. |
| mult_dist_average | Average multiple distance matrices. |
| multSE | Estimate multivariate standard error. |
| parse_amplicon_table | Parse amplicon table |
| parse_fastq_eestats2 | Load USEARCH fastq_eestats2 report |
| parse_funguild | Parse FUNGuild database |
| parse_silva_tax | Split single SILVA taxonomic annotation to taxonomic ranks. |
| parse_silva_tax_batch | Split vector of SILVA taxonomic annotations and prepare... |
| parse_swarms | Parse SWARM files |
| parse_taxonomy_amptk | Parse taxonomy string from AMPtk (for single OTU) |
| parse_taxonomy_amptk_batch | Parse multiple taxonomy strings from AMPtk. |
| parse_uc | Parse UC files (clustering output from USEARCH, VSEARCH,... |
| phred_inverse | Estimate probability of an error based on the Phred-score. |
| phred_score | Estimate Phred Quality Score score from probability of an... |
| phyloseq_add_max_tax_rank | Add the lowest level of taxonomic classification to the... |
| phyloseq_adonis | Permutational multivariate analysis of variance using... |
| phyloseq_average | Average relative OTU abundances. |
| phyloseq_coverage | Estimate the observed abundance-based sample coverage for... |
| phyloseq_coverage_raref | Coverage-based rarefaction |
| phyloseq_effort_div_rangeplot | Vizualize OTU diversity and richness for a particular... |
| phyloseq_extract_non_shared_otus | Extract non-shared species (OTUs) between samples. |
| phyloseq_extract_shared_otus | Extract common species (OTUs) between samples. |
| phyloseq_filter_prevalence | Filter low-prevalence OTUs. |
| phyloseq_filter_sample_wise_abund_trim | Filter rare OTUs based on minimum abundance threshold. |
| phyloseq_filter_taxa_rel_abund | Remove taxa with small mean relative abundance. |
| phyloseq_filter_taxa_tot_fraction | Remove taxa with abundance less then a certain fraction of... |
| phyloseq_filter_top_taxa | Extract the most abundant taxa. |
| phyloseq_filter_top_taxa_range | Check the range of the top-taxa filtering values to determine... |
| phyloseq_group_dissimilarity | Pairwise dissimilarity boxplots. |
| phyloseq_inext | Estimate interpolated and extrapolated Hill numbers and... |
| phyloseq_merge_samples | Merge samples by name |
| phyloseq_mult_raref | Multiple rarefaction of phyloseq-object |
| phyloseq_mult_raref_avg | Perform rarefaction and average relative OTU abundance |
| phyloseq_mult_raref_div | Average diversity estimates across multiple rarefaction... |
| phyloseq_ntaxa_by_tax | Count number of OTUs by taxonomic rank for each sample. |
| phyloseq_num_shared_otus | Estimate the number of shared and non-shared species... |
| phyloseq_otu_appearance | Determine which OTUs appeared or disappeared in comparison... |
| phyloseq_otu_occurrence | Estimate species occurrence (within groups of samples) |
| phyloseq_phylo_div | Estimate phylogenetic diversity (PD), mean pairwise distance... |
| phyloseq_phylo_ses | Estimate standardized effect sizes (SES) of phylogenetic... |
| phyloseq_prevalence_plot | Prevalence plot (total OTU abundance vs OTU prevalence). |
| phyloseq_randomize | Randomize abundance table and phylogeny in phyloseq objects... |
| phyloseq_rename_with_tax | Rename phyloseq OTUs or species with taxonomy ranks. |
| phyloseq_replace_zero | Replace zeros in OTU abundance |
| phyloseq_richness_filter | Remove samples from phyloseq object that have less than n... |
| phyloseq_rm_na_tax | Remove unused taxonomy levels from phyloseq-object. |
| phyloseq_sep_pairwise | Split phyloseq-class object for pairwise comparisons by... |
| phyloseq_sep_samp | Separate phyloseq-class object by sample. |
| phyloseq_sep_tax | Split phyloseq object by taxonomic rank. |
| phyloseq_sep_variable | Split phyloseq-class object by sample-level variable. |
| phyloseq_standardize_otu_abundance | Standardize OTU abundance table |
| phyloseq_summary | Summary for phyloseq objects. |
| phyloseq_taxonomic_resolution | Estimate taxonomic resolution of data |
| phyloseq_to_df | Convert phyloseq object to data frame (for exporting). |
| phyloseq_to_MetaCommunity | Convert phyloseq data to entropart MetaCommunity object. |
| phyloseq_transform_aldex_clr | ALDEx2-based centred log-ratio transformation of OTU table |
| phyloseq_transform_css | Cumulative sum scaling (CSS) normalization of OTU abundance... |
| phyloseq_transform_rlog_blind | Regularized-log (rlog) transformation of OTU abundance table. |
| phyloseq_transform_vst_blind | Variance stabilizing transformation (VST) of OTU abundance... |
| physeq_transform_anderson_log | Log-transformation of OTU abundance table. |
| predict_metagenomes | Produce the actual metagenome functional predictions. |
| prepare_breakaway | Prepare frequency counts for breakaway package |
| prepare_inext | Prepare a list of (corrected) abundance vectors (iNEXT... |
| prevalence | Compute prevalence and abundance summary of each species/OTU. |
| raref_rtk | RTK-based rarefaction |
| read_m8 | Read BLAST output |
| SES | Estimate standardized effect size (SES) and p-value |
| shepard_plot | Plot Shepard diagram |
| some | Check random lines in the data (including phyloseq objects) |
| taxonomy_to_qiime | Prepare taxonomy in QIIME-style |
| uc_to_sumaclust | Convert UC file (clustering output from USEARCH and VSEARCH)... |
