CorrectGapsAndNs: Function to correct an alignment with gaps and Ns

In QSutils: Quasispecies Diversity

Description

Corrects positions in a DNAStringSet or AAStringSet of aligned haplotypes, replacing gaps and Ns (indeterminates) with the nucleotide or amino acid from the corresponding position in the reference sequence.

Usage

CorrectGapsAndNs(hseqs, ref.seq)

Arguments

hseqs	DNAStringSet or AAStringSet object with the alignment to correct.
ref.seq	Character vector with the reference sequence of the alignment.

Value

DNAStringSet or AAStringSet object with the sequences corrected. Duplicate haplotypes may arise as a consequence of this operation. See Recollapse.

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

Recollapse

Examples

# Create a random reference sequence. 
ref.seq <-GetRandomSeq(50)
ref.seq

# Create an alignment with gaps and Ns. 
symb <- c(".","-","N")
nseqs <- 12
p <- c(0.9,0.06,0.04)
hseqs <- matrix(sample(symb,50*nseqs,replace=TRUE,prob=p),ncol=50) 
hseqs <- apply(hseqs,1,paste,collapse="")
hseqs
hseqs <- DNAStringSet(hseqs)

# Apply the function and visualize the result.
cseqs <- CorrectGapsAndNs(hseqs,as.character(ref.seq)) 
c(ref.seq,as.character(cseqs))

QSutils documentation built on Nov. 8, 2020, 7:42 p.m.