Contam_detect {Rbec} | R Documentation

## 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())

[Package Rbec version 1.2.0 Index]