find_dna_tail_per_read: Find poly(A)/poly(T) tail in a single DNA read

In adnaniazi/tailfindr: Poly(A) Tail Length Estimator for Oxford Nanopore RNA and DNA Reads

Find poly(A)/poly(T) tail in a single DNA read

Description

This function finds poly(A) or poly(T) tail length in DNA reads.

Usage

find_dna_tail_per_read(file_path = NA, read_id_fast5_file = NA,
  basecall_group = "Basecall_1D_000", dna_datatype = "cdna",
  save_plots = FALSE, show_plots = FALSE, plot_debug = FALSE,
  save_dir = NA, plotting_library = "rbokeh", multifast5 = FALSE,
  basecalled_with = "albacore", model = "standard", ...)

Arguments

file_path	a character string. Full path of the file that needs to be processed.
read_id_fast5_file	a list. If the read to be processed is in a multi- fast5 file, then a list containing fast5_file path and read_id should be provided, otherwise, it should be set to NA
basecall_group	a character string. Name of the level in the Fast5 file hierarchy from which to read the data e.g. "Basecall_1D_000"
dna_datatype	a character string. Either set to "cdna" or "pcr-dna"
save_plots	a logical. Whether to save plots
show_plots	a logical. Whether to show plots in plots window in R-Studio
plot_debug	a logical. Whether to include debug traces in the plots
save_dir	a logical. Directory where plots should be saved
plotting_library	a character string. Whether to use "rbokeh" or "ggplot2" for plotting the plots
multifast5	a logical. Whether the Fast5 file to be processed is a multifast5 file
basecalled_with	a character. Specify whether the data has been basecalled with the "guppy" or "albacore" software.
model	a character. Specify whether the data has been basecalled using the "standard" or the "flipflop" model
...	Any optional parameter. Reserved for future.

Value

a list

adnaniazi/tailfindr documentation built on March 23, 2024, 7:07 a.m.