Contam_detect {Rbec} | R Documentation |
This function is designed for predicting the contaminated samples
Contam_detect(log_file, outdir, outlier_constant=1.5)
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 |
Ruben Garrido-Oter's group, Plant-Microbe interaction, Max Planck Institute for Plant Breeding Research
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
Pengfan Zhang
#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())