match-utils {Biostrings} | R Documentation |
Utility functions operating on the matches returned by a high-level matching function
Description
Miscellaneous utility functions operating on the matches returned by a
high-level matching function like matchPattern
,
matchPDict
, etc...
Usage
mismatch(pattern, x, fixed=TRUE)
nmatch(pattern, x, fixed=TRUE)
nmismatch(pattern, x, fixed=TRUE)
## S4 method for signature 'MIndex'
coverage(x, shift=0L, width=NULL, weight=1L)
## S4 method for signature 'MaskedXString'
coverage(x, shift=0L, width=NULL, weight=1L)
Arguments
pattern |
The pattern string. |
x |
An XStringViews object for An MIndex object for |
fixed |
See |
shift , width |
See |
weight |
An integer vector specifying how much each element in |
Details
The mismatch
function gives the positions of the mismatching
letters of a given pattern relatively to its matches in a given subject.
The nmatch
and nmismatch
functions give the number of
matching and mismatching letters produced by the mismatch
function.
The coverage
function computes the "coverage" of a subject
by a given pattern or set of patterns.
Value
mismatch
: a list of integer vectors.
nmismatch
: an integer vector containing the length of the vectors
produced by mismatch
.
coverage
: an Rle object indicating
the coverage of x
.
See ?coverage
for the details.
If x
is an MIndex object, the coverage of a given position
in the underlying sequence (typically the subject used during the search
that returned x
) is the number of matches (or hits) it belongs to.
See Also
lowlevel-matching,
matchPattern
,
matchPDict
,
XString-class,
XStringViews-class,
MIndex-class,
coverage,
align-utils
Examples
## ---------------------------------------------------------------------
## mismatch() / nmismatch()
## ---------------------------------------------------------------------
subject <- DNAString("ACGTGCA")
m <- matchPattern("NCA", subject, max.mismatch=1, fixed=FALSE)
mismatch("NCA", m)
nmismatch("NCA", m)
## ---------------------------------------------------------------------
## coverage()
## ---------------------------------------------------------------------
coverage(m)
## See ?matchPDict for examples of using coverage() on an MIndex object...