otucompare: Comparing operational taxonomic unit (OTU) by k-means...

In longreadvqs: Viral Quasispecies Comparison from Long-Read Sequencing Data

Comparing operational taxonomic unit (OTU) by k-means clustering between samples

Description

Pools noise-minimized down-sampled read samples and compares their diversity based on operational taxonomic unit (OTU) classified by k-means clustering of single nucleotide variant (SNV) distance. This function is a subset of "vqscompare" function.

Usage

otucompare(samplelist = list(BC1, BC2, BC3), kmeans.n = 20)

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 operational taxonomic units (OTUs) needed from k-means clustering on multidimensional scale (MDS) of all samples' pairwise genetic distance.

Value

Comparative table of OTU diversity metrics between listed samples calculated from consensus sequence of each OTU by QSutils package

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-----------------------------
sample1 <- vqsassess(sample1filepath, pct = 10, samsize = 20, label = "sample1")
sample2 <- vqsassess(sample2filepath, pct = 10, samsize = 20, label = "sample2")

## Compare OTU (4 clusters) diversity metrics between two samples---------------------------------
otucompare(samplelist = list(sample1, sample2), kmeans.n = 4)

longreadvqs documentation built on Sept. 11, 2024, 6:29 p.m.