longreadvqs (version 0.1.4)

vqsassess: Sequencing error and noise minimization, read down-sampling, and data preparation for viral quasispecies comparison

Description

Minimizes potential long-read sequencing error and noise based on the specified cut-off percentage of low frequency nucleotide base and down-samples read for further comparison with other samples. The output of this function is a list of several objects representing diversity of each sample that must be used as an input for other functions such as "snvcompare" or "vqscompare".

Value

List of 1) "dat": viral quasispecies diversity metrics calculated by QSutils package (similar to "vqssub" function's output), 2) "snvhap": SNV profile of each haplotype with frequency and new label for "vqscompare" function, 3) "snv": plot of SNV frequency for "snvcompare" function, 4) "hapre": DNAStringSet of read alignment of each haplotype for "vqscompare" function, 5) "lab": name of sample or read alignment

Arguments

fasta

Input as a read alignment in FASTA format

method

Sequencing error and noise minimization methods that replace low frequency nucleotide base (less than the "pct" cut-off) with consensus base of that position ("conbase": default) or with base of the dominant haplotype ("domhapbase").

samplingfirst

Downsampling before (TRUE) or after (FALSE: default) the noise minimization.

pct

Percent cut-off defining low frequency nucleotide base that will be replaced (must be specified).

gappct

The percent cut-off particularly specified for gap (-). If it is not specified or less than "pct", "gappct" will be equal to "pct" (default).

ignoregappositions

Replace all nucleotides in the positions in the alignment containing gap(s) with gap. This will make such positions no longer single nucleotide variant (SNV). The default is "FALSE".

samsize

Sample size (number of reads) after down-sampling. If it is not specified or more than number of reads in the original alignment, down-sampling will not be performed (default).

label

String within quotation marks indicating name of read alignment (optional). Please don't use underscore (_) in the label.

Examples

## Locate input FASTA file------------------------------------------------------------------------
sample1filepath <- system.file("extdata", "s1.fasta", package = "longreadvqs")

## Prepare data for viral quasispecies comparison ------------------------------------------------
sample1 <- vqsassess(sample1filepath, pct = 10, samsize = 20, label = "sample1")

## For more examples on other choices of arguments, please see "vqssub" function's examples-------