GetQSData {QSutils} | R Documentation

## Read the aligned sequences, filter at minimum abundance, and sort the sequences

### Description

Reads aligned amplicon sequences with abundance data, filters at a given minimum abundance, and sorts by mutations and abundance.

### Usage

    GetQSData(flnm,min.pct=0.1,type="DNA")

### Arguments

`flnm` | Fasta file with haplotype sequences and their frequencies. The header of each haplotype in the fasta file is composed of an ID followed by a vertical bar "|" followed by the read counts, and eventually followed by another vertical bar and additional information (eg, Hpl.2.0001|15874|25.2).
`min.pct` | Minimum abundance, in %, to filter the reads. Defaults to 0.1%.
`type` | Character string specifying the type of the sequences in the fasta file. This must be one of "DNA" or "AA". It is "DNA" by default.

### Details

The fasta file is loaded and the haplotype abundances, as counts, are taken from the header of each sequence. Haplotypes with abundances below `min.pct` % are filtered out. The haplotypes are then sorted: first, by decreasing order of the number of mutations with respect to the dominant haplotype, and second, by decreasing order of abundances. The haplotypes are then renamed according to the pattern `Hpl.n.xxxx`, where `n` represents the number of mutations, and `xxxx` the abundance order within the mutation number.

### Value

Returns a list with three elements.

`bseqs` | DNAStringSet or AAStringSet with the haplotype sequences.
`nr` | Vector of haplotype counts.
`nm` | Vector of number of mutations of each haplotype with respect to the dominant (most frequent) haplotype.

### Author(s)

Mercedes Guerrero-Murillo and Josep Gregori

### References

Gregori J, Esteban JI, Cubero M, Garcia-Cehic D, Perales C, Casillas R, Alvarez-Tejado M, Rodríguez-Frías F, Guardia J, Domingo E, Quer J. Ultra-deep pyrosequencing (UDPS) data treatment to study amplicon HCV minor variants. PLoS One. 2013 Dec 31;8(12):e83361. doi: 10.1371/journal.pone.0083361. eCollection 2013. PubMed PMID: 24391758; PubMed Central PMCID: PMC3877031.

Ramírez C, Gregori J, Buti M, Tabernero D, Camós S, Casillas R, Quer J, Esteban R, Homs M, Rodriguez-Frías F. A comparative study of ultra-deep pyrosequencing and cloning to quantitatively analyze the viral quasispecies using hepatitis B virus infection as a model. Antiviral Res. 2013 May;98(2):273-83. doi: 10.1016/j.antiviral.2013.03.007. Epub 2013 Mar 20. PubMed PMID: 23523552.

### See Also

`ReadAmplSeqs`

### Examples

    filepath<-system.file("extdata","ToyData_10_50_1000.fna", package="QSutils")
    lst<-GetQSData(filepath,min.pct=0.1,type="DNA")
    lst

[Package QSutils version 1.12.0 Index]