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These functions create user-defined (srFitler) or built-in
instances of SRFilter objects. Filters can be
applied to objects from ShortRead, returning a logical vector
to be used to subset the objects to include only those components
satisfying the filter.
srFilter(fun, name = NA_character_, ...)
"srFilter"(fun, name=NA_character_, ...)
"srFilter"(fun, name=NA_character_, ...)
compose(filt, ..., .name)
idFilter(regex=character(0), fixed=FALSE, exclude=FALSE, .name="idFilter")
occurrenceFilter(min=1L, max=1L, withSread=c(NA, TRUE, FALSE), duplicates=c("head", "tail", "sample", "none"), .name=.occurrenceName(min, max, withSread, duplicates))
nFilter(threshold=0L, .name="CleanNFilter")
polynFilter(threshold=0L, nuc=c("A", "C", "T", "G", "other"), .name="PolyNFilter")
dustyFilter(threshold=Inf, batchSize=NA, .name="DustyFilter")
srdistanceFilter(subject=character(0), threshold=0L, .name="SRDistanceFilter")
##
## legacy filters for ungapped alignments
##
chromosomeFilter(regex=character(0), fixed=FALSE, exclude=FALSE, .name="ChromosomeFilter")
positionFilter(min=-Inf, max=Inf, .name="PositionFilter")
strandFilter(strandLevels=character(0), .name="StrandFilter")
alignQualityFilter(threshold=0L, .name="AlignQualityFilter")
alignDataFilter(expr=expression(), .name="AlignDataFilter")function to be used as a
filter. fun must accept a single named argument x, and
is expected to return a logical vector such that x[fun(x)]
selects only those elements of x satisfying the conditions of
fun
character(1) object to be used as the name of the
filter. The name is useful for debugging and reference.SRFilter object, to be used with
additional arguments to create a composite filter.character(1) object used to over-ride
the name applied to default filters.character(0) or a character(1)
regular expression used as grep(regex, chromosome(x)) to
filter based on chromosome. The default (character(0))
performs no filteringlogical(1) passed to grep,
influencing how pattern matching occurs.logical(1) which, when TRUE, uses
regex to exclude, rather than include, reads.numeric(1)numeric(1). For positionFilter, min
and max define the closed interval in which position must be
found min <= position="" <="max. For occurrenceFilter,
min and max define the minimum and maximum number of
times a read occurs after the filter.character(0) or character(1)
containing strand levels to be selected. ShortRead objects
have standard strand levels NA, "+", "-", "*", with NA
meaning strand information not available and "*" meaning
strand information not relevant.logical(1) indicating whether uniqueness
includes the read sequence (withSread=TRUE), is based only on
chromosome, position, and strand (withSread=FALSE), or only
the read sequence (withSread=NA), as described for
occurrenceFilter below..character{1}, a function name,
or a function taking a single argument. Influence how duplicates are
handled, as described for occurrenceFilter below.numeric(1) value representing a minimum
(srdistanceFilter, alignQualityFilter) or maximum
(nFilter, polynFilter, dustyFilter) criterion
for the filter. The minima and maxima are closed-interval (i.e.,
x >= threshold, x <= threshold<="" code=""> for some property
x of the object being filtered).character vector containing IUPAC symbols for
nucleotides or the value "other" corresponding to all
non-nucleotide symbols, e.g., N.NA or an integer(1) vector indicating
the number of DNA sequences to be processed simultaneously by
dustyFilter. By default, all reads are processed
simultaneously. Smaller values use less memory but are
computationally less efficient.character() of any length, to be used as the
corresponding argument to srdistance.expression to be evaluated with
pData(alignData(x)).srFilter returns an object of SRFilter.Built-in filters return a logical vector of length(x), with
TRUE indicating components that pass the filter. srFilter allows users to construct their own filters. The
fun argument to srFilter must be a function accepting a
single argument x and returning a logical vector that can be
used to select elements of x satisfying the filter with
x[fun(x)]
The signature(fun="missing") method creates a default filter
that returns a vector of TRUE values with length equal to
length(x).
compose constructs a new filter from one or more existing
filter. The result is a filter that returns a logical vector with
indices corresponding to components of x that pass all
filters. If not provided, the name of the filter consists of the names
of all component filters, each separated by " o ".
The remaining functions documented on this page are built-in filters
that accept an argument x and return a logical vector of
length(x) indicating which components of x satisfy the
filter.
idFilter selects elements satisfying
grep(regex, id(x), fixed=fixed).
chromosomeFilter selects elements satisfying
grep(regex, chromosome(x), fixed=fixed).
positionFilter selects elements satisfying
min <= position(x)="" <="max.
strandFilter selects elements satisfying
match(strand(x), strand, nomatch=0) > 0.
occurrenceFilter selects elements that occur >=min and
<=max< code=""> times. withSread determines how reads will be
treated: TRUE to include the sread, chromosome, strand, and
position when determining occurrence, FALSE to include
chromosome, strand, and position, and NA to include only
sread. The default is withSread=NA. duplicates
determines how reads with more than max reads are
treated. head selects the first max reads of each set of
duplicates, tail the last max reads, and sample a
random sample of max reads. none removes all reads
represented more than max times. The user can also provide a
function (as used by tapply) of a single argument to
select amongst reads.
nFilter selects elements with fewer than threshold
'N' symbols in each element of sread(x).
polynFilter selects elements with fewer than threshold
copies of any nucleotide indicated by nuc.
dustyFilter selects elements with high sequence complexity, as
characterized by their dustyScore. This emulates the
dust command from WindowMaker
software. Calculations can be memory intensive; use
batchSize to process the argument to dustyFilter in
batches of the specified size.
srdistanceFilter selects elements at an edit distance greater
than threshold from all sequences in subject.
alignQualityFilter selects elements with alignQuality(x)
greater than threshold.
alignDataFilter selects elements with
pData(alignData(x)) satisfying expr. expr should
be formulated as though it were to be evaluated as
eval(expr, pData(alignData(x))).
SRFilter.sp <- SolexaPath(system.file("extdata", package="ShortRead"))
aln <- readAligned(sp, "s_2_export.txt") # Solexa export file, as example
# a 'chromosome 5' filter
filt <- chromosomeFilter("chr5.fa")
aln[filt(aln)]
# filter during input
readAligned(sp, "s_2_export.txt", filter=filt)
# x- and y- coordinates stored in alignData, when source is SolexaExport
xy <- alignDataFilter(expression(abs(x-500) > 200 & abs(y-500) > 200))
aln[xy(aln)]
# both filters as a single filter
chr5xy <- compose(filt, xy)
aln[chr5xy(aln)]
# both filters as a collection
filters <- c(filt, xy)
subsetByFilter(aln, filters)
summary(filters, aln)
# read, chromosome, strand, position tuples occurring exactly once
aln[occurrenceFilter(withSread=TRUE, duplicates="none")(aln)]
# reads occurring exactly once
aln[occurrenceFilter(withSread=NA, duplicates="none")(aln)]
# chromosome, strand, position tuples occurring exactly once
aln[occurrenceFilter(withSread=FALSE, duplicates="none")(aln)]
# custom filter: minimum calibrated base call quality >20
goodq <- srFilter(function(x) {
apply(as(quality(x), "matrix"), 1, min, na.rm=TRUE) > 20
}, name="GoodQualityBases")
goodq
aln[goodq(aln)]
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