Contam_detect: Reference-based error correction of amplicon sequencing data

In PengfanZhang/Rbec: Rbec: a tool for analysis of amplicon sequencing data from synthetic microbial communities

Reference-based error correction of amplicon sequencing data

Description

This function is designed for predicting the contaminated samples

Usage

Contam_detect(log_file, outdir, outlier_constant=1.5)

Arguments

log_file	the file contains a list of log files of each sample outputted with Rbec function
outdir	output directory
outlier_constant	the multiplier of variance to define the outlier

Details

Ruben Garrido-Oter's group, Plant-Microbe interaction, Max Planck Institute for Plant Breeding Research

Value

Returns a plot showing the distribution of percentage of corrected reads across the whole sample set and a summary file recording which samples might be contaminated

Author(s)

Pengfan Zhang

Examples

#log_file <- system.file("extdata", "rbec_test.list", package = "Rbec")
log_path <- list.files(paste(path.package("Rbec"), 
	"extdata/contamination_test", sep="/"), 
	recursive=TRUE, full.names=TRUE)
log_file <- tempfile()
writeLines(log_path, log_file)
Contam_detect(log_file, tempdir())

PengfanZhang/Rbec documentation built on Sept. 13, 2023, 1 a.m.