findOverlaps: Find features overlapping GWAS markers

In aaronwolen/bingd: Bayesian integration of genomic data

Description

Determine which GWAS markers overlap each FeatureList feature.

Usage

## S4 method for signature 'GWAS,FeatureList'
findOverlaps(query, subject, maxgap = 0L,
  minoverlap = 1L, type = c("any", "start", "end", "within"),
  select = c("all", "first", "last", "arbitrary"), ignore.strand = FALSE)

Arguments

query	GWAS object
subject	FeatureList object
maxgap	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.
minoverlap	see documentation for maxgap argument
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.
select	When select is "all" (the default), the results are returned as a Hits object. When select is "first", "last", or "arbitrary" the results are returned as an integer vector of length query containing the first, last, or arbitrary overlapping interval in subject, with NA indicating intervals that did not overlap any intervals in subject. If select is "all", a Hits object is returned. For all other select the return value depends on the drop argument. When select != "all" && !drop, an IntegerList is returned, where each element of the result corresponds to a space in query. Whenselect != "all" && drop, an integer vector is returned containing indices that are offset to align with the unlisted query.
ignore.strand	When set to TRUE, the strand information is ignored in the overlap calculations.

Value

findOverlaps returns either a HitsList-class object when select="all" (the default), or a CompressedIntegerList when select is not "all".

aaronwolen/bingd documentation built on May 10, 2019, 4:04 a.m.