IntersectMatrix function

Intersect genomic coordinates with matrix rows

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

Returns

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)