Signac (version 0.2.4)

GetIntersectingFeatures: Find interesecting regions between two objects

Description

Intersects the regions stored in the rownames of two objects and returns a vector containing the names of rows that interesect for each object. The order of the row names return corresponds to the intersecting regions, ie the nth feature of the first vector will intersect the nth feature in the second vector. A distance parameter can be given, in which case features within the given distance will be called as intersecting.

Usage

GetIntersectingFeatures(
  object.1,
  object.2,
  assay.1 = NULL,
  assay.2 = NULL,
  distance = 0,
  sep.1 = c("-", "-"),
  sep.2 = c("-", "-"),
  verbose = TRUE
)

Arguments

object.1

The first Seurat object

object.2

The second Seurat object

assay.1

Name of the assay to use in the first object. If NULL, use the default assay

assay.2

Name of the assay to use in the second object. If NULL, use the default assay

distance

Maximum distance between regions allowed for an intersection to be recorded. Default is 0.

sep.1

Genomic coordinate separators to use for the first object

sep.2

Genomic coordinate separators to use for the second object

verbose

Display messages

Value

Returns a list of two character vectors containing the row names in each object that overlap each other.

Examples

# NOT RUN {
GetIntersectingFeatures(
  object.1 = atac_small,
  object.2 = atac_small,
  assay.1 = 'peaks',
  assay.2 = 'bins',
  sep.1 = c(":", "-"),
  sep.2 = c("-", "-")
)
# }