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,
...
)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 |
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)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.