align_details: A universal parameter settings object for Rsubread alignment

In compbiomed/MetaScope: Tools and functions for preprocessing 16S and metagenomic sequencing microbiome data

A universal parameter settings object for Rsubread alignment

Description

This object is a named vector of multiple options that can be chosen for functions that involve alignment with Rsubread, namely align_target() and filter_host(). Both functions take an object for the parameter settings, which are provided by align_details by default, or may be given by a user-created object containing the same information.

Usage

data(align_details)

Format

list

Details

The default options included in align_details are type = "dna", maxMismatches = 3, nsubreads = 10, phredOffset = 33, unique = FALSE, and nBestLocations = 16. Full descriptions of these parameters can be read by accessing ?Rsubread::align.

Examples

data("align_details")

compbiomed/MetaScope documentation built on Nov. 30, 2024, 4:35 p.m.