featureOverlaps: Find features overlapping GWAS markers

In aaronwolen/bingd: Bayesian integration of genomic data

Description

Determine which GWAS markers overlap each FeatureList feature.

Usage

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

## S4 method for signature 'GWAS,FeatureList'
featureOverlaps(query, subject, maxgap = 0L,
  minoverlap = 1L, type = c("any", "start", "end", "within"), ...)

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.
...	Further arguments to be passed to or from other methods: drop: All methods accept the drop argument (FALSE by default). See select argument above for the details. ignoreSelf, ignoreRedundant: When subject is omitted, the ignoreSelf and ignoreRedundant arguments (both FALSE by default) are allowed. See query and subject arguments above for the details.

Value

A list of DataFrames, the structure of which mirrors that of the supplied FeatureList object. Each element of the list is a DataFrame with one logical vector for each feature, indicating marker overlap.

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