ApplyPileupsParam {Rsamtools} | R Documentation

## Parameters for creating pileups from BAM files

### Description

Use `ApplyPileupsParam()` to create a parameter object influencing what fields and which records are used to calculate pile-ups, and to influence the values returned.

### Usage

    # Constructor
    ApplyPileupsParam(flag = scanBamFlag(),
        minBaseQuality = 13L, minMapQuality = 0L,
        minDepth = 0L, maxDepth = 250L,
        yieldSize = 1L, yieldBy = c("range", "position"), yieldAll = FALSE,
        which = GRanges(), what = c("seq", "qual"))

    # Accessors
    plpFlag(object)
    plpFlag(object) <- value
    plpMaxDepth(object)
    plpMaxDepth(object) <- value
    plpMinBaseQuality(object)
    plpMinBaseQuality(object) <- value
    plpMinDepth(object)
    plpMinDepth(object) <- value
    plpMinMapQuality(object)
    plpMinMapQuality(object) <- value
    plpWhat(object)
    plpWhat(object) <- value
    plpWhich(object)
    plpWhich(object) <- value
    plpYieldAll(object)
    plpYieldAll(object) <- value
    plpYieldBy(object)
    plpYieldBy(object) <- value
    plpYieldSize(object)
    plpYieldSize(object) <- value

    ## S4 method for signature 'ApplyPileupsParam'
    show(object)

### Arguments

`flag` | An instance of the object returned by `scanBamFlag`, restricting various aspects of reads to be included or excluded.
`minBaseQuality` | The minimum read base quality below which the base is ignored when summarizing pileup information.
`minMapQuality` | The minimum mapping quality below which the entire read is ignored.
`minDepth` | The minimum depth of the pile-up below which the position is ignored.
`maxDepth` | The maximum depth of reads considered at any position; this can be used to limit memory consumption.
`yieldSize` | The number of records to include in each call to `FUN`.
`yieldBy` | How records are to be counted. By range (in which case `yieldSize` must equal 1) means that `FUN` is invoked once for each range in `which`. By position means that `FUN` is invoked whenever pile-ups have been accumulated for `yieldSize` positions, regardless of ranges in `which`.
`yieldAll` | Whether to report all positions (`yieldAll=TRUE`), or just those passing the filtering criteria of `flag`, `minBaseQuality`, etc. When `yieldAll=TRUE`, positions not passing filter criteria have ‘0’ entries in `seq` or `qual`.
`which` | A `GRanges` or `IntegerRangesList` instance restricting pileup calculations to the corresponding genomic locations.
`what` | A `character()` instance indicating what values are to be returned. One or more of `c("seq", "qual")`.
`object` | An instace of class `ApplyPileupsParam`.
`value` | An instance to be assigned to the corresponding slot of the `ApplyPileupsParam` instance.

### Objects from the Class

Objects are created by calls of the form `ApplyPileupsParam()`.

### Slots

Slot interpretation is as described in the ‘Arguments’ section.

`flag`

  Object of class `integer` encoding flags to be kept when they have their '0' (`keep0`) or '1' (`keep1`) bit set.

`minBaseQuality`

  An `integer(1)`.

`minMapQuality`

  An `integer(1)`.

`minDepth`

  An `integer(1)`.

`maxDepth`

  An `integer(1)`.

`yieldSize`

  An `integer(1)`.

`yieldBy`

  An `character(1)`.

`yieldAll`

  A `logical(1)`.

`which`

  A `GRanges` or `IntegerRangesList` object.

`what`

  A `character()`.

### Functions and methods

See 'Usage' for details on invocation.

Constructor:

ApplyPileupsParam:

  Returns a `ApplyPileupsParam` object.

Accessors: get or set corresponding slot values; for setters, `value` is coerced to the type of the corresponding slot.

plpFlag, plpFlag<-

  Returns or sets the named `integer` vector of flags; see `scanBamFlag`.

plpMinBaseQuality, plpMinBaseQuality<-

  Returns or sets an `integer(1)` vector of miminum base qualities.

plpMinMapQuality, plpMinMapQuality<-

  Returns or sets an `integer(1)` vector of miminum map qualities.

plpMinDepth, plpMinDepth<-

  Returns or sets an `integer(1)` vector of miminum pileup depth.

plpMaxDepth, plpMaxDepth<-

  Returns or sets an `integer(1)` vector of the maximum depth to which pileups are calculated.

plpYieldSize, plpYieldSize<-

  Returns or sets an `integer(1)` vector of yield size.

plpYieldBy, plpYieldBy<-

  Returns or sets an `character(1)` vector determining how pileups will be returned.

plpYieldAll, plpYieldAll<-

  Returns or sets an `logical(1)` vector indicating whether all positions, or just those satisfying pileup positions, are to be returned.

plpWhich, plpWhich<-

  Returns or sets the object influencing which locations pileups are calculated over.

plpWhat, plpWhat<-

  Returns or sets the `character` vector describing what summaries are returned by pileup.

Methods:

show

  Compactly display the object.

### Author(s)

Martin Morgan

### See Also

applyPileups.

### Examples

    example(applyPileups)

[Package Rsamtools version 2.10.0 Index]