longreadvqs (version 0.1.4)

vqssub: Computing viral quasispecies diversity metrics of noise-minimized down-sampled read alignment

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 summary of viral quasispecies diversity metrics calculated by QSutils package's functions. This function is a subset of "vqsassess" function.

Value

Data frame containing all viral quasispecies diversity metrics calculated by QSutils package, noise minimization, and down-sampling information.

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).

Examples

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

## Summarize viral quasispecies diversity metrics--------------------------------------------------
# From noise-minimized unsampled reads (10% cut-off):
vqssub(fastafilepath, pct = 10, label = "sample1")
# From noise-minimized sampled reads (n = 20):
vqssub(fastafilepath, pct = 10, samsize = 20, label = "sample1")
# From noise-minimized sampled reads with 50% cut-off for gap:
vqssub(fastafilepath, pct = 10, gappct = 50, samsize = 20, label = "sample1")
# From noise-minimized sampled reads but ignore positions with gap:
vqssub(fastafilepath, pct = 10, ignoregappositions = TRUE, samsize = 20, label = "sample1")
# From reads that were down-sampled before noise minimization:
vqssub(fastafilepath, pct = 10, samplingfirst = TRUE, samsize = 20, label = "sample1")