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

Description Usage Arguments Details Value Note Author(s) See Also Examples

View source: R/DBA.R

Description

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

Usage

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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

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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

Bioconductor-mirror/DiffBind documentation built on July 14, 2017, 7:48 a.m.