srFilter {ShortRead} | R Documentation

## Functions for user-created and built-in ShortRead filters

### Description

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.

### Usage

    srFilter(fun, name = NA_character_, ...)
    ## S4 method for signature 'missing'
    srFilter(fun, name=NA_character_, ...)
    ## S4 method for signature 'function'
    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")

### Arguments

`fun` | An object of class `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`
`name` | A `character(1)` object to be used as the name of the filter. The `name` is useful for debugging and reference.
`filt` | A `SRFilter` object, to be used with additional arguments to create a composite filter.
`.name` | An optional `character(1)` object used to over-ride the name applied to default filters.
`regex` | Either `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 filtering
`fixed` | `logical(1)` passed to `grep`, influencing how pattern matching occurs.
`exclude` | `logical(1)` which, when `TRUE`, uses `regex` to exclude, rather than include, reads.
`min` | `numeric(1)`
`max` | `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.
`strandLevels` | Either `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.
`withSread` | A `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..
`duplicates` | Either `character{1}`, a function `name`, or a function taking a single argument. Influence how duplicates are handled, as described for `occurrenceFilter` below.
`threshold` | A `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` for some property `x` of the object being filtered).
`nuc` | A `character` vector containing IUPAC symbols for nucleotides or the value `"other"` corresponding to all non-nucleotide symbols, e.g., `N`.
`batchSize` | `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.
`subject` | A `character()` of any length, to be used as the corresponding argument to `srdistance`.
`expr` | A `expression` to be evaluated with `pData(alignData(x))`.
`...` | Additional arguments for subsequent methods; these arguments are not currently used.

### Details

`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` 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)))`.

### Value

`srFilter` returns an object of `SRFilter`.

Built-in filters return a logical vector of `length(x)`, with `TRUE` indicating components that pass the filter.

### Author(s)

Martin Morgan <mtmorgan@fhcrc.org>

### See Also

`SRFilter`.

### Examples

    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)]

[Package ShortRead version 1.45.4 Index]