single_consensus_byBarcode: Compute SINGLE consensus

In rocioespci/single: Accurate consensus sequence from nanopore reads of a gene library

Compute SINGLE consensus

Description

Main function to compute consensus after correcting reads by a SINGLE model.

Usage

single_consensus_byBarcode(
  barcodes_table,
  sequences,
  readID_col = 1,
  bcID_col = 2,
  header = TRUE,
  dec = ".",
  sep = " ",
  verbose = TRUE
)

Arguments

barcodes_table	data.frame or file name containing the names of the reads and the barcode associated (or any grouping tag).
sequences	QualityScaledDNAStringSet or fastq file name. Contains sequences from which compute weighted consensus.
readID_col, bcID_col	Numeric. Columns where the reads id and the barcode (or grouping tag) are, in the barcodes_table
header, dec, sep	Arguments for read.table(barcodes_table)
verbose	Logical.

Value

DNAStringSet with consensus sequences

Examples

pos_start=1
pos_end = 100
barcodes_file =  system.file("extdata", "Barcodes_table.txt",package = "single")
reads_single = system.file("extdata", "corrected_seqs.fastq", package = "single")
single_consensus_byBarcode(barcodes_file,reads_single, verbose = FALSE)

rocioespci/single documentation built on April 18, 2023, 8:48 p.m.