combineReadTrackingTablesITS: Combine ITS Read-Tracking Tables

In claraqin/neonMicrobe: Downloading, Pre-processing, and Assembling NEON Soil Microbe Marker Gene Sequence Data

Combine ITS Read-Tracking Tables

Description

Convenience function for combining the read-tracking tables across the trimming, filtering, and DADA steps of the ITS processing pipeline.

Usage

combineReadTrackingTablesITS(prefilter_table, filter_table, dada_table)

Arguments

filter_table	Read-tracking table output by qualityFilterITS.
dada_table	Read-tracking table output by runDadaITS.
trim_table	Read-tracking table output by trimPrimersITS.

Value

An integer matrix with columns representing each step in the DADA2 ITS processing pipeline, and rows representing each input sample, with values representing the read counts remaining at that step for each sample.

claraqin/neonMicrobe documentation built on April 11, 2024, 11:47 a.m.