region_overlap: Region overlap

In fortune9/ZZMisc: A bag of useful functions that have not found home package

Region overlap

Description

Given two lists of genomic regions, a data.table containing the overlapped regions are returned.

Usage

region_overlap(
  x,
  y,
  regionCols1 = 1:3L,
  regionCols2 = 1:3L,
  type = c("any", "within", "start", "end", "equal"),
  mult = c("all", "first", "last"),
  matchedOnly = F
)

Arguments

x	The first input genomic regions. A data.frame() or data.table().
y	The second input genomic regions. A data.frame() or data.table().
regionCols1	A vector of column names or numbers in x giving 'chr', 'start', and 'end' columns in order. Default is the first 3 columns.
regionCols2	A vector of column names or numbers in y giving 'chr', 'start', and 'end' columns in order. Default is the first 3 columns.
type	Default value is any. Allowed values are any, within, start, end and equal. The types shown here are identical in functionality to the function findOverlaps in the bioconductor package IRanges. Let [a,b] and [c,d] be intervals in x and y with a<=b and c<=d. For type="start", the intervals overlap iff a == c. For type="end", the intervals overlap iff b == d. For type="within", the intervals overlap iff a>=c and b<=d. For type="equal", the intervals overlap iff a==c and b==d. For type="any", as long as c<=b and d>=a, they overlap. In addition to these requirements, they also have to satisfy the minoverlap argument as explained above. NB: maxgap argument, when > 0, is to be interpreted according to the type of the overlap. This will be updated once maxgap is implemented.
mult	When multiple rows in y match to the row in x, mult=. controls which values are returned - "all" (default), "first" or "last".
matchedOnly	A logical. If TRUE, then non-overlaped input regions won't be output. If FALSE (default), all the rows are output

Details

The input genomic regions should contain 3 columns, 'chr', 'start', and 'end', and all other columns are copied to the output.

Value

A data.table. The columns from x and y will have suffix '.x' and '.y', respectively.

fortune9/ZZMisc documentation built on July 1, 2022, 9:43 a.m.