Construct a genomic range query for a GTable with a genomic range index

Usage

genomicRangeQuery(chr, lo, hi, mode = "overlap", index = "gri")

Arguments

chr

Chromosome name

lo

Integer low coordinate

hi

Integer high coordinate

mode

The type of query to perform: "overlap" (default) or "enclose"

index

The name of the genomic range index to use

Examples

genomicRangeQuery("chrI", 1000, 5000)
$index
[1] "gri"

$parameters
$parameters$mode
[1] "overlap"

$parameters$coords
$parameters$coords[[1]]
[1] "chrI"

$parameters$coords[[2]]
[1] 1000

$parameters$coords[[3]]
[1] 5000




genomicRangeQuery("chrII", 1000, 10000, mode="enclose", index="othergri")
$index
[1] "othergri"

$parameters
$parameters$mode
[1] "enclose"

$parameters$coords
$parameters$coords[[1]]
[1] "chrII"

$parameters$coords[[2]]
[1] 1000

$parameters$coords[[3]]
[1] 10000

See also