0.5.0

metagMisc v.0.5.0 (git 621e9cf, March 20, 2024)

• New functions

  • phyloseq_num_shared_otus.R - estimation of the number of shared and non-shared OTUs between all pairwise combinations of samples
  • phyloseq_bootstrap - bootstraps samples in phyloseq object
  • phyloseq_combine_samples - sums OTU abundances of replicates or sample groups into a single sample
  • phyloseq_coverage - estimates the observed abundance-based sample coverage
  • coverage_to_samplesize - estimates the required sample size for a particular coverage
  • phyloseq_coverage_raref - coverage-based rarefaction
  • phyloseq_effort_div - computes OTU diversity for a particular sample size or coverage
  • phyloseq_effort_div_rangeplot - vizualization of OTU diversity and richness for a particular sequencing depth or sample coverage ranges
  • phyloseq_otu_appearance - determines which OTUs appeared or disappeared in comparison with reference sample group
  • phyloseq_richness_filter - removes samples from phyloseq object that have less than n taxa
  • phyloseq_inext - estimates interpolated and extrapolated Hill numbers and sample coverage and constructs rarefaction curve
  • phyloseq_merge_samples - merges samples by name
  • phyloseq_mult_raref_dist - performs multiple rarefactions and averages sample dissimilarity across rarefactions
  • phyloseq_rename_with_tax - renames phyloseq OTUs or species with taxonomy ranks
  • phyloseq_sep_pairwise - splits phyloseq-class object for pairwise comparisons by sample-level variable
  • phyloseq_taxonomic_resolution - summarizes taxonomic resolution of the data
  • phyloseq_taxonomy_imputation - replaces missing taxonomy with higher ranks
  • phyloseq_replace_zero - replaces zeros in OTU abundance with psudocount or min observed abundnce
  • phyloseq_transform_aldex_clr - performs ALDEx2-based centred log-ratio transformation of OTU table
  • get_max_taxonomic_rank_DT - determines the lowest level of taxonomic classification (with data.table)
  • prepare_breakaway - prepares frequency counts for breakaway package
  • raref_rtk - RTK-based rarefaction
  • read_m8 - reads the standard BLAST m8 format (-outfmt 6)
  • blast_to_wide - converts BLAST results to a wide table
  • SES - standardized effect size estimation
  • centroid_coords - coordinates of centroids and medoids
  • chunk - split vector into chunks of equal size
  • chunk_table - split data.table into chunks
  • count_primers - counts number of reads in which the primer is found
  • jaccard_bray - converts between Bray-Curtis and Jaccard dissimilarity indicies
  • leading_zero - adds or removes leading zeros
  • zero_pad - pads a number with leading zeros
  • package_availability - checks the availability of dependencies
  • vegdist_zero - Bray-Curtis index with double-zero support

• Bug fixes

  • phyloseq_extract_shared_otus and phyloseq_extract_non_shared_otus - issue warning in the case if no OTUs were found
  • get_max_taxonomic_rank - data types bug
  • phyloseq_average - progress bar fixed
  • parse_uc - fixed a column name problem
  • prevalence was added to NAMESPACE (thanks @LukDrey for reporting the issue)

• The other updates

  • phyloseq_to_df - handles taxa as rows case and checks the presence of taxonomy in phyloseq object
  • parse_uc - is much faster now with data.table
  • parse_uc - new option to remove duplicated rows
  • parse_taxonomy_amptk rewritten
  • parse_taxonomy_amptk_batch - supports multithreading now
  • phyloseq_standardize_otu_abundance - added wisconsin and rhea methods
  • phyloseq_filter_prevalence - informative error messages added
  • phyloseq_sep_variable - informative error messages added
  • phyloseq_summary - add OTU occurrence stats
  • eig_perc - added plots of explained variance percentages
  • adonis_pairwise
  • phyloseq_ntaxa_by_tax
  • some - works with phyloseq now
  • taxonomy_to_qiime - supports Domain rank and performs validation of user-supplied ranks
  • phyloseq_otu_occurrence - added counts
  • phyloseq_filter_sample_wise_abund_trim - added relative abundance option
  • phyloseq_phylo_ses - added VPD metric
  • phyloseq_group_dissimilarity - added comparison types (between/within group)
  • phyloseq_extract_shared_otus - estimates percentage of shared OTUs
  • prevalence is now much faster with data.table

• New logo, designed by Olesya Dulya

• Documentation updates