Toy.GapsAndNs.fna {QSutils} | R Documentation

## Fasta file with raw reads with gaps and Ns

### Description

Fasta file of sequenced data with some missing information. This is toy data to illustrate some functions of the package `QSutils` package.

### Format

Fasta file format. Each sequence starts with the symbol ">" followed by the sequence ID. Subsequent lines correspond to the nucleotide sequences or peptide sequences.

### See Also

`Collapse`, `CorrectGapsAndNs` and `Recollapse`

### Examples

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

    lstCollapsed <- Collapse(reads)
    DottedAlignment(lstCollapsed$hseqs)
    lstCorrected<-CorrectGapsAndNs(lstCollapsed$hseqs[2:length(lstCollapsed$hseqs)],
                    lstCollapsed$hseqs[[1]])
    lstCorrected<- c(lstCollapsed$hseqs[1],lstCorrected)
    lstCorrected
    lstRecollapsed<-Recollapse(lstCorrected,lstCollapsed$nr)
    lstRecollapsed

[Package QSutils version 1.12.0 Index]