GetQSData: Read the aligned sequences, filter at minimum abundance, and...

In VHIRHepatiques/QSutils: Quasispecies Diversity

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

VHIRHepatiques/QSutils documentation built on April 27, 2024, 10:29 p.m.