dba.mask: Derive a mask to define a subset of peaksets or sites for a...

In DiffBind: Differential Binding Analysis of ChIP-Seq Peak Data

Description

Derives a mask to define a subset of peaksets or sites for a DBA object.

Usage

dba.mask(DBA, attribute, value, combine='or', mask, merge='or', bApply=FALSE,
         peakset, minValue=-1)

Arguments

DBA	DBA object
attribute	when deriving a peakset mask, attribute to base mask on: DBA_ID DBA_TISSUE DBA_FACTOR DBA_CONDITION DBA_TREATMENT DBA_REPLICATE DBA_CONSENSUS DBA_CALLER DBA_CONTROL

value	when deriving a peakset/sample mask, attribute value (or vector of attribute values) to match.
combine	when deriving a peakset/sample mask, if value is a vector, OR when deriving a site mask, and peaksets is a vector, this is method for combining result of each value: “or” “and” “nor” “nand”
mask	when deriving a peakset/sample mask, this specifies an existing mask to merge with; if missing, create new mask
merge	when deriving a peakset/sample mask, and an existing mask is supplied, this specifies the method for combining new mask with supplied mask: “or” “and” “nor” “nand” note: if mask is missing, “nand” results in negative of mask
bApply	when deriving a peakset/sample mask, a logical indicating that a new DBA object with the mask applied will be returned.
peakset	when deriving a peak/site mask, this specifies a peakset number, or a vector of peakset numbers. The resulting mask will indicate which of the overall sites were called as peaks in this peakset or set of peaksets. If a vector, the masks for each of the peaksets will be combined using the method specified in the combine parameter.
minValue	when deriving a peak/site mask, scores greater than this value will be considered as indicating that the site corresponds to a called peakset.

Details

MODE: Derive a a mask of peaksets/samples:

dba.mask(DBA, attribute, value, combine, mask, merge, bApply)

MODE: Derive a mask of peaks/sites:

dba.mask(DBA, combine, mask, merge,bApply, peakset, minValue)

Value

either a logical mask, or new DBA object if bApply is TRUE.

Note

dba automatically generates masks for each unique value of DBA_TISSUE, DBA_FACTOR, DBA_CONDITION, DBA_TREATMENT, DBA_CALLER, and DBA_REPLICATE. These are accessible using masks field of the DBA object (DBA$masks), and can be viewed using names(DBA$masks).

Author(s)

Rory Stark

See Also

dba.show

Examples

data(tamoxifen_peaks)

# Pre-made masks
names(tamoxifen$masks)
dba.show(tamoxifen,tamoxifen$masks$MCF7)

# New masks
mcf7Mask <- dba.mask(tamoxifen,DBA_TISSUE, "MCF7")
mcf7DerivedMask <- dba.mask(tamoxifen,DBA_TISSUE,"TAMR",mask=mcf7Mask)
mcf7Derived <- dba(tamoxifen,mcf7DerivedMask)
mcf7Derived

DiffBind documentation built on March 24, 2021, 6 p.m.