A DNAString object allows efficient storage and manipulation of a long DNA sequence.
The DNAString class is a direct XString subclass (with no additional slot). Therefore all functions and methods described in the XString man page also work with a DNAString object (inheritance).
Unlike the BString container that allows storage of any single string (based on a single-byte character set) the DNAString container can only store a string based on the DNA alphabet (see below). In addition, the letters stored in a DNAString object are encoded in a way that optimizes fast search algorithms.
This alphabet contains all letters from the
IUPAC Extended Genetic Alphabet (see
"-" (the gap letter),
"+" (the hard
masking letter), and
"." (the not a letter or not
It is stored in the
DNA_ALPHABET predefined constant (character
alphabet() function returns
applied to a DNAString object.
In the code snippet below,
x can be a single string (character vector of length 1),
a BString object or an RNAString object.
DNAString(x="", start=1, nchar=NA):
Tries to convert
x into a DNAString object by reading
nchar letters starting at position
In the code snippet below,
x is a DNAString object.
x is a DNAString object, then return the DNA
alphabet (see above).
See the corresponding man pages when
x is a
BString, RNAString or AAString object.
The letters in a DNAString object are colored when displayed by the
show() method. Set global option
to FALSE to turn off this coloring.
The DNAStringSet class to represent a collection of DNAString objects.
The XString and RNAString classes.
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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': Filter, Find, Map, Position, Reduce, anyDuplicated, append, as.data.frame, basename, cbind, colMeans, colSums, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which, 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  "A" "C" "G" "T"  "A" "C" "G" "T" "M" "R" "W" "S" "Y" "K" "V" "H" "D" "B" "N" "-" "+" "." 13-letter "DNAString" instance seq: TTGAAAA-CTC-N  13  "A" "C" "G" "T" "M" "R" "W" "S" "Y" "K" "V" "H" "D" "B" "N" "-" "+" "."  "A" "C" "G" "T"
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