Pad and clip strings
padAndClip first conceptually pads the supplied strings with an
infinite number of padding letters on both sides, then clip them.
stackStrings is a convenience wrapper to padAndClip
that turns a variable-width set of strings into a rectangular
(i.e. constant-width) set, by padding and clipping the strings,
after conceptually shifting them horizontally.
padAndClip(x, views, Lpadding.letter=" ", Rpadding.letter=" ",
remove.out.of.view.strings=FALSE)
stackStrings(x, from, to, shift=0L,
Lpadding.letter=" ", Rpadding.letter=" ",
remove.out.of.view.strings=FALSE)x |
An XStringSet object containing the strings to pad and clip. |
views |
A IntegerRanges object (recycled to the length of
|
Lpadding.letter, Rpadding.letter |
A single letter to use for padding on the left, and another one to
use for padding on the right. Note that the default letter ( |
remove.out.of.view.strings |
|
from, to |
Another way to specify the region to keep for each string, but with
the restriction that |
shift |
An integer vector (recycled to the length of |
For padAndClip: An XStringSet object.
If remove.out.of.view.strings is FALSE, it has the same
length and names as x, and its "shape", which is described by the
integer vector returned by width(), is the same as the shape of the
views argument after recycling.
The class of the returned object is the direct concrete subclass of
XStringSet that x belongs to or derives from.
There are 4 direct concrete subclasses of the XStringSet virtual
class: BStringSet, DNAStringSet, RNAStringSet,
and AAStringSet. If x is an instance of one of
those classes, then the returned object has the same class as x
(i.e. in that case, padAndClip acts as an endomorphism).
But if x derives from one of those 4 classes, then the
returned object is downgraded to the class x derives from.
In that case, padAndClip does not act as an endomorphism.
For stackStrings: Same as padAndClip. In addition it is
guaranteed to have a rectangular shape i.e. to be a constant-width
XStringSet object.
H. Pagès
The stackStringsFromBam function
in the GenomicAlignments package for stacking the read
sequences (or their quality strings) stored in a BAM file on
a region of interest.
The XStringViews class to formally represent a set of views on a single string.
The extractAt and replaceAt functions
for extracting/replacing arbitrary substrings from/in a string or
set of strings.
The XStringSet class.
The IntegerRanges class in the IRanges package.
x <- BStringSet(c(seq1="ABCD", seq2="abcdefghijk", seq3="", seq4="XYZ"))
padAndClip(x, IRanges(3, 8:5), Lpadding.letter=">", Rpadding.letter="<")
padAndClip(x, IRanges(1:-2, 7), Lpadding.letter=">", Rpadding.letter="<")
stackStrings(x, 2, 8)
stackStrings(x, -2, 8, shift=c(0, -11, 6, 7),
Lpadding.letter="#", Rpadding.letter=".")
stackStrings(x, -2, 8, shift=c(0, -14, 6, 7),
Lpadding.letter="#", Rpadding.letter=".")
stackStrings(x, -2, 8, shift=c(0, -14, 6, 7),
Lpadding.letter="#", Rpadding.letter=".",
remove.out.of.view.strings=TRUE)
library(hgu95av2probe)
probes <- DNAStringSet(hgu95av2probe)
probes
stackStrings(probes, 0, 26,
Lpadding.letter="+", Rpadding.letter="-")
options(showHeadLines=15)
stackStrings(probes, 3, 23, shift=6*c(1:5, -(1:5)),
Lpadding.letter="+", Rpadding.letter="N",
remove.out.of.view.strings=TRUE)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.