ReadAmplSeqs: Read a fasta file with haplotypes and frequencies

In VHIRHepatiques/QSutils: Quasispecies Diversity

Read a fasta file with haplotypes and frequencies

Description

Loads an alignment of haplotypes and their frequencies from a fasta file.

Usage

ReadAmplSeqs(flnm,type="DNA")

Arguments

flnm	File name of a 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 count, and eventually followed by another vertical bar and additional information (eg, Hpl.2.0001|15874|25.2).
type	Character string specifying the types of sequences in the fasta file. This must be either "DNA" or "AA". It is "DNA" by default.

Value

Returns a list with two elements:

nr	Vector of the haplotype counts.
hseqs	DNAStringSet or AAStringSet with the haplotype DNA sequences or amino acid sequences.

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

GetQSData

Examples

filepath<-system.file("extdata","ToyData_10_50_1000.fna", package="QSutils")
lst <- ReadAmplSeqs(filepath,type="DNA")
lst

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