GenoGAM (version 1.0.2)

subsetByOverlaps,GenoGAMDataSet,GRanges-method: Subset by overlaps method for GenoGAMDataSet

Description

Subsetting the GenoGAMDataSet by a GRanges object

Usage

"subsetByOverlaps"(query, subject, maxgap = 0L, minoverlap = 1L, type = c("any", "start", "end", "within", "equal"), ...)

Arguments

query

A GenoGAMDataSet object.

subject

A GRanges object

maxgap, minoverlap

Intervals with a separation of maxgap or less and a minimum of minoverlap overlapping positions, allowing for maxgap, are considered to be overlapping. maxgap should be a scalar, non-negative, integer. minoverlap should be a scalar, positive integer.

type

By default, any overlap is accepted. By specifying the type parameter, one can select for specific types of overlap. The types correspond to operations in Allen's Interval Algebra (see references). If type is start or end, the intervals are required to have matching starts or ends, respectively. While this operation seems trivial, the naive implementation using outer would be much less efficient. Specifying equal as the type returns the intersection of the start and end matches. If type is within, the query interval must be wholly contained within the subject interval. Note that all matches must additionally satisfy the minoverlap constraint described above.

The maxgap parameter has special meaning with the special overlap types. For start, end, and equal, it specifies the maximum difference in the starts, ends or both, respectively. For within, it is the maximum amount by which the query may be wider than the subject.

...

Additional parameters

Value

A subsetted GenoGAMDataSet object.

Examples

ggd <- makeTestGenoGAMDataSet()
gr <- GRanges("chrI", IRanges(1,50))
res <- subsetByOverlaps(ggd, gr)