align-utils {Biostrings} | R Documentation |
A variety of different functions used to deal with sequence alignments.
nedit(x) # also nmatch and nmismatch mismatchTable(x, shiftLeft=0L, shiftRight=0L, ...) mismatchSummary(x, ...) ## S4 method for signature 'AlignedXStringSet0': coverage(x, start=NA, end=NA, shift=0L, width=NULL, weight=1L) ## S4 method for signature 'PairwiseAlignedFixedSubject': coverage(x, start=NA, end=NA, shift=0L, width=NULL, weight=1L) compareStrings(pattern, subject) ## S4 method for signature 'PairwiseAlignedFixedSubject': consensusMatrix(x, baseOnly=FALSE, freq=FALSE, gapCode="-", endgapCode="-")
x |
A character vector or matrix, XStringSet , XStringViews ,
PairwiseAlignedXStringSet , or list of FASTA records containing
the equal-length strings.
|
shiftLeft, shiftRight |
Non-positive and non-negative integers respectively that specify how many preceding and succeeding characters to and from the mismatch position to include in the mismatch substrings. |
... |
Further arguments to be passed to or from other methods. |
start, end, shift, width |
See ?coverage .
|
weight |
An integer vector specifying how much each element in x counts.
|
pattern, subject |
The strings to compare. Can be of type character , XString ,
XStringSet , AlignedXStringSet , or, in the case of
pattern , PairwiseAlignedXStringSet . If pattern is a
PairwiseAlignedXStringSet object, then subject must be
missing.
|
baseOnly |
TRUE or FALSE .
If TRUE , the returned vector only contains frequencies for the
letters in the "base" alphabet i.e. "A", "C", "G", "T" if x
is a "DNA input", and "A", "C", "G", "U" if x is "RNA input".
When x is a BString object (or an XStringViews
object with a BString subject, or a BStringSet object),
then the baseOnly argument is ignored.
|
freq |
If TRUE , then letter frequencies (per position) are reported,
otherwise counts.
|
gapCode, endgapCode |
The codes in the appropriate alphabet to use for the internal
and end gaps.
|
mismatchTable
: a data.frame containing the positions and substrings
of the mismatches for the AlignedXStringSet
or
PairwiseAlignedXStringSet
object.
mismatchSummary
: a list of data.frame objects containing counts and
frequencies of the mismatches for the AlignedXStringSet
or
PairwiseAlignedFixedSubject
object.
compareStrings
combines two equal-length strings that are assumed to be
aligned into a single character string containing that replaces mismatches
with "?"
, insertions with "+"
, and deletions with "-"
.
pairwiseAlignment
,
consensusMatrix
,
XString-class, XStringSet-class, XStringViews-class,
AlignedXStringSet-class, PairwiseAlignedXStringSet-class,
match-utils
## Compare two globally aligned strings string1 <- "ACTTCACCAGCTCCCTGGCGGTAAGTTGATC---AAAGG---AAACGCAAAGTTTTCAAG" string2 <- "GTTTCACTACTTCCTTTCGGGTAAGTAAATATATAAATATATAAAAATATAATTTTCATC" compareStrings(string1, string2) ## Create a consensus matrix nw1 <- pairwiseAlignment(AAStringSet(c("HLDNLKGTF", "HVDDMPNAL")), AAString("SMDDTEKMSMKL"), substitutionMatrix = "BLOSUM50", gapOpening = -3, gapExtension = -1) consensusMatrix(nw1) ## Examine the consensus between the bacteriophage phi X174 genomes data(phiX174Phage) phageConsmat <- consensusMatrix(phiX174Phage, baseOnly = TRUE) phageDiffs <- which(apply(phageConsmat, 2, max) < length(phiX174Phage)) phageDiffs phageConsmat[,phageDiffs]