lysis_rate: A lysis_rate Function

In kevinzhongxu/tslysis: A package to estimate taxon-specific microbial lysis

A lysis_rate Function

Description

This function allows calculating both the taxon-specific lysis and lysis rate of microbe, based on the input of a tabular-separated otu table (.txt) and metadata (.txt) The otu_table contains data from three rDNA/rRNA fractions (Cellular rDNA, Cellular rRNA and Extracellular rRNA) of each water sample. The metadata contains contains at least columns "sample.id", "Abundance_Total_Cellular.rRNA", "Abundance_Total_Extracellular.rRNA" and "turnover_rate".

Usage

lysis_rate(otu_table, metadata)

Arguments

otu_table	'Path/To/Your/OTU_TABLE_FILE'; For example: otu_table="/home/kevin/Desktop/data/10reads-plus/otu_table_qiime2_otu_16S.txt".
metadata	'Path/To/Your/METADATA_FILE'; For example: metadata="/home/kevin/Desktop/data/10reads-plus/metadata.txt".

Examples

##### If you want to estimate both the taxon-specific lysis and lysis rate for prokaryotes, then run
lysis_rate(otu_table="Path/To/Your/OTU_TABLE_FILE_16S.txt", metadata="Path/To/Your/METADATA.txt")

kevinzhongxu/tslysis documentation built on Feb. 23, 2025, 11:12 a.m.