getInteractionMatrix: Compute interaction matrix

In bkaczkowski/xcore: xcore expression regulators inference

Compute interaction matrix

Description

getInteractionMatrix construct interaction matrix between two Granges objects. Names of object a became row names and names of b column names.

Usage

getInteractionMatrix(a, b, ext = 500, count = FALSE)

Arguments

a	GRanges object.
b	GRanges object.
ext	Integer specifying number of base pairs the a coordinates should be extended in upstream and downstream directions.
count	Logical indicating if matrix should hold number of overlaps between a and b or if FALSE presence / absence indicators.

Value

Sparse matrix of class dgCMatrix, with rows corresponding to a and columns to b. Each cell holds a number indicating how many times a and b overlapped.

Examples

a <- GenomicRanges::GRanges(
  seqnames = c("chr20", "chr4"),
  ranges = IRanges::IRanges(
    start = c(62475984L, 173530220L),
    end = c(62476001L, 173530236L)),
  strand = c("-", "-"),
  name = c("hg19::chr20:61051039..61051057,-;hg_188273.1",
           "hg19::chr4:174451370..174451387,-;hg_54881.1"))
b <- GenomicRanges::GRanges(
  seqnames = c("chr4", "chr20"),
  ranges = IRanges::IRanges(
    start = c(173530229L, 63864270L),
    end = c(173530236L, 63864273L)),
  strand = c("-", "-"),
  name = c("HAND2", "GATA5"))
getInteractionMatrix(a, b)

bkaczkowski/xcore documentation built on Jan. 26, 2024, 6:24 p.m.