Toy.GapsAndNs.fna: Fasta file with raw reads with gaps and Ns

In VHIRHepatiques/QSutils: Quasispecies Diversity

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

VHIRHepatiques/QSutils documentation built on April 12, 2024, 12:25 p.m.