Intersect genomic coordinates with matrix rows

Source: R/utilities.R

Remove or retain matrix rows that intersect given genomic regions

IntersectMatrix(
  matrix,
  regions,
  invert = FALSE,
  sep = c("-", "-"),
  verbose = TRUE,
  ...
)

Arguments

matrix

A matrix with genomic regions in the rows
regions

A set of genomic regions to intersect with regions in the matrix. Either a vector of strings encoding the genomic coordinates, or a GRanges object.
invert

Discard rows intersecting the genomic regions supplied, rather than retain.
sep

A length-2 character vector containing the separators to be used for extracting genomic coordinates from a string. The first element will be used to separate the chromosome name from coordinates, and the second element used to separate start and end coordinates.
verbose

Display messages
...

Additional arguments passed to findOverlaps

Value

Returns a sparse matrix

Examples

counts <- matrix(data = rep(0, 12), ncol = 2)
rownames(counts) <- c("chr1-565107-565550","chr1-569174-569639",
"chr1-713460-714823","chr1-752422-753038",
"chr1-762106-763359","chr1-779589-780271")
IntersectMatrix(matrix = counts, regions = blacklist_hg19)

#> Intersecting genomic regions
#> Subsetting matrix
#>                    [,1] [,2]
#> chr1-565107-565550    0    0
#> chr1-569174-569639    0    0
#> chr1-713460-714823    0    0