Remove or retain matrix rows that intersect given genomic regions
IntersectMatrix(
matrix,
regions,
invert = FALSE,
sep = c("-", "-"),
verbose = TRUE,
...
)A matrix with genomic regions in the rows
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.
Discard rows intersecting the genomic regions supplied, rather than retain.
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.
Display messages
Additional arguments passed to findOverlaps
Returns a sparse matrix
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