Description Usage Arguments Details Value Author(s) References See Also Examples
Reads aligned amplicon sequences with abundance data, filters at a given minimum abundance, and sorts by mutations and abundance.
1 |
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. |
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.
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. |
Mercedes Guerrero-Murillo and Josep Gregori
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.
1 2 3 | filepath<-system.file("extdata","ToyData_10_50_1000.fna", package="QSutils")
lst<-GetQSData(filepath,min.pct=0.1,type="DNA")
lst
|
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