ToyData_10_50_1000.fna: Fasta file with 10 haplotypes, 50 basepairs in size.

Description Format Examples

Description

Fasta file that contains the sequence of 10 haplotypes used as examples in the 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.

Examples

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filepath<-system.file("extdata","ToyData_10_50_1000.fna", package="QSutils")
lst <- ReadAmplSeqs(filepath,type="DNA")
lst

Example output

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

Attaching package:BiocGenericsThe following objects are masked frompackage:parallel:

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

The following objects are masked frompackage:stats:

    IQR, mad, sd, var, xtabs

The following objects are masked frompackage: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:S4VectorsThe following object is masked frompackage:base:

    expand.grid

Loading required package: IRanges
Loading required package: XVector

Attaching package:BiostringsThe following object is masked frompackage:base:

    strsplit

$nr
 [1] 464  62  39  27  37  16  33  54 248  20

$hseqs
DNAStringSet object of length 10:
     width seq                                              names               
 [1]    50 CACCCTGTGACCAGTGTGTGCGA...GTGCCCCGTTGGCATTGACTAT Hpl_0_0001|464|46.4
 [2]    50 CACTCTGTGACCAGTGTGTGCGA...GTGCCCCGTTGGCATTGACTAT Hpl_1_0001|62|6.2
 [3]    50 CACCCTGTGACCAGCGTGTGCGA...GTGCCCCGTTGGCATTGACTAT Hpl_1_0002|39|3.9
 [4]    50 CACCCTGTGACCAGTGTGTGCGA...GTGCCCCGTTGGCATTGACTAC Hpl_1_0003|27|2.7
 [5]    50 CACTCTGTGACCAGTGTGTGCGA...GTGCCCCGTTAGCATTGACTAT Hpl_2_0001|37|3.7
 [6]    50 CACTCGGTGACCAGTGTGCGTGA...GTGCCCCGTTGGCATTGACTAT Hpl_4_0001|16|1.6
 [7]    50 CACTCTGTGACCAGTGTGCGCGA...GTGCCCTGTCGGCATTGACTAT Hpl_5_0001|33|3.3
 [8]    50 CACTCTGTGATCAGTGTGCGCGA...GTGCCCTGCCGGCATCGACTAT Hpl_8_0001|54|5.4
 [9]    50 CACTCTGTGATCAGTGTGCGCGA...GTGCCCTGCCGGCATCGACTAC Hpl_9_0001|248|24.8
[10]    50 CACTCTGTGATCAGTGTGCGCGA...GTGCCCTGCCGGCACCGACTAC Hpl_10_0001|20|2

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