eDNAfuns (version 0.1.0)

eDNAindex: Create scaled relative proportions of the number of reads of taxa in different samples

Description

This function takes a long ASV table (tibble) and creates a new column with the relative proportions scaled to their maximum, to avoid the dominance of species with better primer efficiency

Usage

eDNAindex(
  tibble,
  Sample_column = Sample,
  OTU_column = Hash,
  Counts_column = nReads,
  Biological_replicate_column = NULL,
  ...
)

Value

A tibble with at least the columns Sample_column, OTU_column and Normalized.reads

Arguments

tibble

A tibble the ASV table in a long format, with at least three columns, Sample_column, OTU_column, Counts_column

Sample_column

The column indicating the sample.

OTU_column

The column indicating the OTU/ASV.

Counts_column

The column (numeric) with the number of sequences from that OTU in that sample.

Biological_replicate_column

The column representing replicate measurements of Sample_column.

...

Any extra columns that want to be added to the final dataset (either taxonomical information about OTUs, or metadata information about the samples)

Examples

data("training.ASV.table")
eDNAindex(training.ASV.table, Sample_column = Sample_name)