Package index • micro4R

All functions

assess_example: Larger example dataset for further runs

assess_run(): Assess sequencing results

calcBeta(): Calculate beta diversity dissimilarities with or without rarefaction

checkAll(): checker utils in this section Check your ASV count and taxonomy tables, and optionall metadata, for potential issues.

checkMeta(): Check metadata file to identify potential downstream issues. DEPRECATED

checkSampleID(): Simple function to check for a column called SampleID

contaminate(): "Contaminate" the example ASV table so decontam can run in example

converter(): Converts tibbles, data frames, and matrices to each other as needed by the specific function

dada2_asvtable(): dada2 workflow to generate ASV table

dada2_decontam_wrapper(): Wrapper of entire dada2/decontam process

dada2_taxa(): dada2 taxa

dada2_wrapper(): dada2 wrapper

decontam_wrapper(): Decontam

exampleData: List of all three example objects in one package

example_metadata(): Load in example metadata file

filtering(): Filter the ASV table

known_dada2_dbs(): A simple tibble of the names of maintained dada2-formatted taxonomy reference databases

makeExample(): Create example data for testing and teaching purposes specifically for this package.

makeExampleMeta(): Create a simple metadata table

makeExampleSeqtab(): Creates a simple example ASV table

makeExampleTaxa(): Create a simple taxonomy table

packItUp(): Package up your three objects (metadata, asvtable, taxonomy table) into a single list for less typing

ref_db(): Set a reference database for taxonomy assignment

test_dbs(): Load test databases into environment without having to type so much. Because I'm lazy and got really tired of finding the exact text to copy paste

tibblefy(): tibblefy a specific type of data frame. DEPRECATED. use converter() instead

unsampled_example(): Load in unsampled example

whereFastqs(): Collection of helper/utility functions not really intended to be directly used by end user Path to user's fastq file folder