CorrectGapsAndNs {QSutils} | R Documentation

## Function to correct an alignment with gaps and Ns

### 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))

[Package QSutils version 1.0.0 Index]