pctopt: Optimizing cut-off percentage for noise minimization

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

Optimizing cut-off percentage for noise minimization

Description

Finds an optimal cut-off percentage for noise minimization (in vqssub, vqsassess, and vqscustompct functions) that can decrease the number of singleton haplotypes to less than the desired percentage of the total reads.

Arguments

fasta	Input as a read alignment in FASTA format
pctsing	The desired percentage of singleton haplotypes relative to the total reads in the alignment.
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.
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).

Value

An optimal cut-off percentage for noise minimization of an input sample and parameter settings. If label is specified, the output will be a data frame with percentage of singleton haplotypes at each cut-off percentage from zero to the optimal cut-off percentage.

Examples

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

## Find an cut-off percentage that creates singleton haplotypes less than 50% of the alignment.----
pctopt(fastafilepath, pctsing = 50, label = "s1")

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