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
|
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
|
yieldBy |
How records are to be counted. By range (in which case
|
yieldAll |
Whether to report all positions
( |
which |
A |
what |
A |
object |
An instace of class |
value |
An instance to be assigned to the corresponding slot of
the |
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
orIntegerRangesList
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; seescanBamFlag
.- 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
Examples
example(applyPileups)