outseq: Get the final denoised output sequence for a read.

In debar: A Post-Clustering Denoiser for COI-5P Barcode Data

Get the final denoised output sequence for a read.

Description

Get the final denoised output sequence for a read.

Usage

outseq(x, ...)

## S3 method for class 'DNAseq'
outseq(x, ..., keep_flanks = TRUE, ambig_char = "N",
  adjust_limit = 5)

Arguments

x	a DNAseq class object.
...	additional arguments to be passed between methods.
keep_flanks	Should the regions of the input sequence outside of the barcode region be readded to the denoised sequence prior to outputting to the file. Options are TRUE, FALSE and 'right'. The 'right' option will keep the trailing flank but remove the leading flank. Default is TRUE. False will lead to only the denoised sequence for the 657bp barcode region being output to the file.
ambig_char	The character to use for ambigious positions in the sequence.
adjust_limit	the maximum number of corrections that can be applied to a sequence read. If this number is exceeded then the entire read is masked with ambigious characters. Default is 5.

Value

a class object of code "ccs_reads"

See Also

DNAseq

frame

adjust

Examples

#previously run
excess_string = paste0("CCCCCC", example_nt_string_errors, 
                       "CCCCCCCC", collapse="")
ex_data = DNAseq(excess_string, name = 'ex1')
ex_data =  frame(ex_data)
ex_data = adjust(ex_data)
#build output sequence with trimmed edges
ex_data = outseq(ex_data, keep_flanks = TRUE)
ex_data$outseq #view the output sequence, edges were reattached
#you will avoid data loss on edge of sequence, but errors in edge, or
#off target sequence will be present in the output
#
#build output sequence with only the COI-5P region
ex_data = outseq(ex_data, keep_flanks = FALSE)
ex_data$outseq #view the output sequence
#Ns added to the front to buffer trimmed region
#Note some sequence is lost due to the strange 
#path match that occurs at the front of the sequence.
ex_data$data$path

debar documentation built on May 29, 2024, 2:02 a.m.