Function reference • metabaR

Import / Format Generate `metabarlist objects` from files of various formats or directly from R objects
`tabfiles_to_metabarlist()`	Import 4 tables to create a metabarlist object
`obifiles_to_metabarlist()`	Import OBITools and associated files to create a metabarlist object
`biomfiles_to_metabarlist()`	Import BIOM and associated files to create a metabarlist object
`read_ngsfilter()`	Import an ngsfilter file
`metabarlist_generator()`	Create a metabarlist object
`check_metabarlist()`	Checks if a list of tables is a `metabarlist`
`silva_annotator()`	Including SILVAngs pipeline taxonomic annotations
`silva_annotator_deprec()`	Including SILVAngs pipeline taxonomic annotations
Visualise Visualise data under both ecological and experimental perspectives
`summary_metabarlist()`	Metabarlist summary
`ggpcrplate()`	Plotting a PCR attribute in the PCR plate design
`ggpcrtag()`	Plotting a PCR attribute in the tag pair design
`ggtaxplot()`	Plotting a taxonomic tree
`hill_rarefaction()` `gghill_rarefaction()`	Generating rarefaction curves using Hill numbers
`pcrslayer()` `pcr_within_between()` `FUN_pcrdist_bray_freq()` `FUN_pcrdist_coa_freq()` `check_pcr_thresh()` `pcr_threshold_estimate()` `check_pcr_repl()`	Detecting PCRs replicate outliers.
Manipulate Manipulate `metabarlist` objects
`subset_metabarlist()`	Subsetting metabarlists
`extract_table()`	Extract tables from a `metabarlist` object
`aggregate_pcrs()` `FUN_agg_pcrs_sum()` `FUN_agg_pcrs_mean()` `FUN_agg_pcrs_prob()`	Aggregate PCR replicates
`aggregate_motus()` `FUN_agg_motus_sum()`	Aggregate MOTUs
`taxoparser()`	Parse taxonomic information
`taxodecider()`	Selecting the correct taxonomy
Flag spurious signal Detect and enable the tagging of potential molecular artifacts such as contaminants or failed PCR reactions
`contaslayer()`	Detecting contaminants using negative controls
`tagjumpslayer()`	Filtering potential tag-jumps in metabarcoding data
`pcrslayer()` `pcr_within_between()` `FUN_pcrdist_bray_freq()` `FUN_pcrdist_coa_freq()` `check_pcr_thresh()` `pcr_threshold_estimate()` `check_pcr_repl()`	Detecting PCRs replicate outliers.
`pcr_outlier()` `filter_replicat()` `coa_function()` `bray_function()`	Identify non-conforming PCR replicates
Export Export data in fasta format
`fasta_generator()`	Generating a fasta file from a `metabarlist` object
Example data set
`soil_euk`	Soil eukaryote DNA metabarcoding data from French Guiana

Reference

Import / Format

Visualise

Manipulate

Flag spurious signal

Export

Example data set