vqsout: Exporting viral quasispecies profile comparison results

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

Exporting viral quasispecies profile comparison results

Description

Writes out resulting objects from "vqscompare" function as tables (TSV files) and alignment (FASTA file) to the working directory.

Usage

vqsout(vqscompare.obj, directory = "path/to/directory")

Arguments

vqscompare.obj	A resulting object from "vqscompare" function.
directory	Path to desired directory (location) for output files. If it is not specified, the directory will be the current working directory.

Value

TSV files of viral quasispecies profile comparison results and FASTA file of unique haplotype alignment.

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 = 0, samsize = 50, label = "sample1")
sample2 <- vqsassess(sample2filepath, pct = 0, samsize = 50, label = "sample2")

## Compare viral quasispecies and OTU (4 clusters) diversity between two samples------------------
comp <- vqscompare(samplelist = list(sample1, sample2),
           lab_name = "Sample", kmeans.n = 4, showhap.n = 5)

## Export Key outputs from "vqscompare" function--------------------------------------------------
notrun <- vqsout(comp, directory = tempdir())

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