subsetDerep: Subset a derep-class based on abundance of the reads

In carlopacioni/amplicR: An R package to process amplicon data

Subset a derep-class based on abundance of the reads

Description

This function retains the reads that have their abundance >= minAbund. It returns an object similar to a derep-class in its structure. Indeed it has a $uniques and quals elemnt for the retained sequences, but, rather than having map as third element in the list, it has rmed, which is a vector with the index of the positions of the uniques from the original object that were removed.

Usage

subsetDerep(derep, minAbund = 2)

Arguments

derep	The derep object to subset
minAbund	The threshold below which reads are removed

Value

A list where the first two elements are as a derep-class, and the third is rmed. See details.

carlopacioni/amplicR documentation built on Aug. 19, 2023, 7:59 p.m.