Collapse {QSutils} | R Documentation

## Collapse reads into haplotypes and frequencies

### Description

Collapse summarizes aligned reads into haplotypes with their frequencies. Recollapse is used to update the collapse after some type of manipulation may have resulted in duplicate haplotypes.

### Usage

    Collapse(seqs)
    Recollapse(seqs,nr)

### Arguments

`seqs` | DNAStringSet or AAStringSet object with the sequences to collapse.
`nr` | Vector with the haplotype counts.

### Details

Recollapse is used when haplotypes may become equivalent after some type of manipulation. It removes duplicate sequences and updates their frequencies.

### Value

Collapse and Recollapse return a list with two elements.

`nr` | Vector of the haplotype counts.
`hseqs` | DNAStringSet or AAStringSet with the haplotype sequence.

### 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.

### Examples

    # Load raw reads.
    filepath<-system.file("extdata","Toy.GapsAndNs.fna", package="QSutils")
    reads <- readDNAStringSet(filepath)

    # Collapse this reads into haplotypes
    lstCollapsed <- Collapse(reads)
    lstCorrected<-CorrectGapsAndNs(lstCollapsed$hseqs[2:length(lstCollapsed$hseqs)],
                    lstCollapsed$hseqs[[1]])
    #Add again the most abundant haplotype.
    lstCorrected<- c(lstCollapsed$hseqs[1],lstCorrected)
    lstCorrected
    # Recollapse the corrected haplotypes
    lstRecollapsed<-Recollapse(lstCorrected,lstCollapsed$nr)
    lstRecollapsed

[Package QSutils version 1.2.0 Index]