trimTails {ShortRead} | R Documentation |
These generic functions remove leading or trailing nucleotides or
qualities. trimTails
and trimTailw
remove low-quality
reads from the right end using a sliding window (trimTailw
) or
a tally of (successive) nucleotides falling at or below a quality
threshold (trimTails
). trimEnds
takes an alphabet of
characters to remove from either left or right end.
trimTailw(object, k, a, halfwidth, ..., ranges=FALSE) ## S4 method for signature 'BStringSet' trimTailw(object, k, a, halfwidth, ..., alphabet, ranges=FALSE) ## S4 method for signature 'XStringQuality' trimTailw(object, k, a, halfwidth, ..., ranges=FALSE) trimTails(object, k, a, successive=FALSE, ..., ranges=FALSE) ## S4 method for signature 'BStringSet' trimTails(object, k, a, successive=FALSE, ..., alphabet, ranges=FALSE) ## S4 method for signature 'XStringQuality' trimTails(object, k, a, successive=FALSE, ..., ranges=FALSE) trimEnds(object, a, left=TRUE, right=TRUE, relation=c("<=", "=="), ..., ranges=FALSE) ## S4 method for signature 'XStringSet' trimEnds(object, a, left=TRUE, right=TRUE, relation=c("<=", "=="), ..., ranges=FALSE) ## S4 method for signature 'XStringQuality' trimEnds(object, a, left=TRUE, right=TRUE, relation=c("<=", "=="), ..., ranges=FALSE) ## S4 method for signature 'FastqQuality' trimEnds(object, a, left=TRUE, right=TRUE, relation=c("<=", "=="), ..., ranges=FALSE) ## S4 method for signature 'ShortRead' trimEnds(object, a, left=TRUE, right=TRUE, relation=c("<=", "=="), ..., ranges=FALSE) ## S4 method for signature 'ShortReadQ' trimEnds(object, a, left=TRUE, right=TRUE, relation=c("<=", "=="), ..., ranges=FALSE)
object |
An object for which a methods exist (e.g.,
|
k |
|
a |
For For |
halfwidth |
The half width (cycles before or after the current; e.g., a half-width of 5 would span 5 + 1 + 5 cycles) in which qualities are assessed. |
successive |
|
left, right |
|
relation |
|
... |
Additional arguments, perhaps used by methods. |
alphabet |
|
ranges |
|
trimTailw
starts at the left-most nucleotide, tabulating the
number of cycles in a window of 2 * halfwidth + 1
surrounding
the current nucleotide with quality scores that fall at or below
a
. The read is trimmed at the first nucleotide for which this
number >= k
. The quality of the first or last nucleotide is
used to represent portions of the window that extend beyond the
sequence.
trimTails
starts at the left-most nucleotide and accumulates
cycles for which the quality score is at or below a
. The read
is trimmed at the first location where this number >= k
. With
successive=TRUE
, failing qualities must occur in strict
succession.
trimEnds
examines the left
, right
, or both ends
of object
, marking for removal letters that correspond to
a
and relation
. The trimEnds,ShortReadQ-method
trims based on quality.
An instance of class(object)
trimmed to contain only those
nucleotides satisfying the trim criterion or, if ranges=TRUE
an
IRanges
instance defining the ranges that would trim
object
.
Martin Morgan <mtmorgan@fhcrc.org>
showMethods(trimTails) sp <- SolexaPath(system.file('extdata', package='ShortRead')) rfq <- readFastq(analysisPath(sp), pattern="s_1_sequence.txt") ## remove leading / trailing quality scores <= 'I' trimEnds(rfq, "I") ## remove leading / trailing 'N's rng <- trimEnds(sread(rfq), "N", relation="==", ranges=TRUE) narrow(rfq, start(rng), end(rng)) ## remove leading / trailing 'G's or 'C's trimEnds(rfq, c("G", "C"), relation="==")