DecodeR: Barcode Prediction

In tangchao7498/DecodeR: Barcode demultiplexing of native RNAs nanopore sequencing

Barcode Prediction

Description

Barcode Prediction

Usage

DecodeR(
  fast5,
  model,
  NT = 1,
  cutoff = 0,
  include.lowest = FALSE,
  clear = FALSE
)

Arguments

fast5	path to a fast5 file
model	a trained model for prediction
NT	the number of cores to use, i.e. at most how many child processes will be run simultaneously.
cutoff	the cutoff of minimum probability for classified reads, high for accuracy, low for recovery
include.lowest	include.lowest of cutoff
clear	TRUE for a clear output

Examples

fast5file <- system.file("extdata/demo2_0.fast5", package = "DecodeR")
data("Model_2barcodes")

pred <- DecodeR(fast5 = fast5file, model = Model_2barcodes)
hist(pred$Probability, xlab = "Probability", main = "Histogram of Probability")
table(pred$Barcode)

pred2 <- DecodeR(fast5 = fast5file, model = Model_2barcodes, cutoff = 0.8)
table(pred2$Barcode)

tangchao7498/DecodeR documentation built on May 27, 2023, 7:21 p.m.