Rsamtools: ApplyPileupsParam-class – R documentation

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ApplyPileupsParam-class

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

Examples

example(applyPileups)

Rsamtools

Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import

v2.6.0

Artistic-2.0 | file LICENSE

Authors

Martin Morgan, Hervé Pagès, Valerie Obenchain, Nathaniel Hayden

Initial release