longreadvqs (version 0.1.4)

AAcompare: Comparing viral quasispecies diversity metrics at amino acid level

Description

Pools noise-minimized down-sampled read samples and compares their diversity metrices based on protein haplotype and single amino acid variation (SAV) group that is classified by k-means clustering of SAV distance. This function is a subset of "vqscompare" function.

Usage

AAcompare(
  samplelist = list(BC1, BC2, BC3),
  kmeans.n = 20,
  removestopcodon = FALSE
)

Value

List of 1) "aadiv": comparative table of viral quasispecies diversity metrics between listed samples based on translated reads calculated by QSutils package, and 2) "savgrpdiv": comparative table of single amino acid (SAV) group diversity metrics between listed samples calculated from consensus amino acid sequence of each SAV group

Arguments

samplelist

List of samples, i.e., name of resulting objects from "vqsassess" or "vqscustompct" functions, for example list(BC1, BC2, BC3).

kmeans.n

Number of single amino acid variation (SAV) groups needed from k-means clustering on multidimensional scale (MDS) of all samples' pairwise SAV distance.

removestopcodon

Remove the last amino acid (expected to be a stop codon) from translated amino acid sequences before further analysis (optional). If not specified or if removestopcodon = FALSE, the last amino acid will not be removed (default).

Examples

## Locate input FASTA files-----------------------------------------------------------------------
sample1filepath <- system.file("extdata", "s1.fasta", package = "longreadvqs")
sample2filepath <- system.file("extdata", "s2.fasta", package = "longreadvqs")

## Prepare data for viral quasispecies comparison between two samples-----------------------------
set.seed(123)
sample1 <- vqsassess(sample1filepath, pct = 5, samsize = 50, label = "sample1")
sample2 <- vqsassess(sample2filepath, pct = 5, samsize = 50, label = "sample2")

## Compare protein haplotype and SAV group (4 clusters) diversity metrics between two samples-----
AAcompare(samplelist = list(sample1, sample2), kmeans.n = 4)