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

In QSutils: Quasispecies Diversity

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

Example output

Loading required package: Biostrings
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, basename, cbind, colnames,
    dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
    grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
    rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:base’:

    expand.grid

Loading required package: IRanges
Loading required package: XVector

Attaching package: ‘Biostrings’

The following object is masked from ‘package:base’:

    strsplit

                                                   1 
"TGACGCGCACAGAGTGCTGCTAAATGACTGGGTTACCCCGTCGTGGTCGC" 
                                                   2 
"......-..........................................." 
                                                   3 
".....................-............................" 
                                                   4 
"........................-........................." 
                                                   5 
"........................................-........." 
                                                   6 
"..........................................-......." 
                                                   7 
"......N..........................................." 
                                                   8 
"-.......................................-........." 
                                                   9 
".-................................................" 
                                                  10 
"..-...........................-..................." 
                                                  11 
"....-.......-................-...................." 
                                                  12 
"..........-......................................." 
                                                  13 
"...............-.................................." 
                                                  14 
"......................-.........N................." 
                                                  15 
"........................N...........-.....N......." 
                                                  16 
"..........................-......................." 
                                                  17 
"...........................-..-..................." 
                                                  18 
"...............................-.................." 
                                                  19 
"................................N................." 
                                                  20 
"..............................................N..." 
                                                  21 
"................................................-." 
                                                  22 
"................................................N." 
                                                  23 
"..........................................N......." 
                                                  24 
"..........................................N......N" 
                                                  25 
".........................................N........" 
                                                  26 
"..................................N.N............." 
                                                  27 
"...............................N.-................" 
                                                  28 
"...........................N......................" 
                                                  29 
".........................N........................" 
                                                  30 
"......................N..........................." 
                                                  31 
"................N................................." 
                                                  32 
".............N......................N............." 
                                                  33 
"........N........................................." 
                                                  34 
".....N............................................" 
DNAStringSet object of length 34:
     width seq                                              names               
 [1]    50 TGACGCGCACAGAGTGCTGCTAA...TGGGTTACCCCGTCGTGGTCGC 1
 [2]    50 TGACGCGCACAGAGTGCTGCTAA...TGGGTTACCCCGTCGTGGTCGC 2
 [3]    50 TGACGCGCACAGAGTGCTGCTAA...TGGGTTACCCCGTCGTGGTCGC 3
 [4]    50 TGACGCGCACAGAGTGCTGCTAA...TGGGTTACCCCGTCGTGGTCGC 4
 [5]    50 TGACGCGCACAGAGTGCTGCTAA...TGGGTTACCCCGTCGTGGTCGC 5
 ...   ... ...
[30]    50 TGACGCGCACAGAGTGCTGCTAA...TGGGTTACCCCGTCGTGGTCGC 30
[31]    50 TGACGCGCACAGAGTGCTGCTAA...TGGGTTACCCCGTCGTGGTCGC 31
[32]    50 TGACGCGCACAGAGTGCTGCTAA...TGGGTTACCCCGTCGTGGTCGC 32
[33]    50 TGACGCGCACAGAGTGCTGCTAA...TGGGTTACCCCGTCGTGGTCGC 33
[34]    50 TGACGCGCACAGAGTGCTGCTAA...TGGGTTACCCCGTCGTGGTCGC 34
$nr
[1] 100

$seqs
DNAStringSet object of length 1:
    width seq                                               names               
[1]    50 TGACGCGCACAGAGTGCTGCTAA...CTGGGTTACCCCGTCGTGGTCGC 1

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