Closest Feature

Find the closest feature to a given set of genomic regions

ClosestFeature(object, regions, annotation = NULL, ...)

Arguments

object	A Seurat object
regions	A set of genomic regions to query
annotation	A GRanges object containing annotation information. If NULL, use the annotations stored in the object.
...	Additional arguments passed to StringToGRanges

Value

Returns a dataframe with the name of each region, the closest feature in the annotation, and the distance to the feature.

Examples

# \donttest{
ClosestFeature(
  object = atac_small,
  regions = head(granges(atac_small))
)
#>                             tx_id    gene_name         gene_id gene_biotype
#> ENSE00001787178   ENST00000450983 RP4-669L17.2 ENSG00000236601      lincRNA
#> ENSE00001787178.1 ENST00000450983 RP4-669L17.2 ENSG00000236601      lincRNA
#> ENSE00001787178.2 ENST00000450983 RP4-669L17.2 ENSG00000236601      lincRNA
#> ENSE00001787178.3 ENST00000450983 RP4-669L17.2 ENSG00000236601      lincRNA
#> ENSE00001787178.4 ENST00000450983 RP4-669L17.2 ENSG00000236601      lincRNA
#> ENSE00001787178.5 ENST00000450983 RP4-669L17.2 ENSG00000236601      lincRNA
#>                   type     closest_region       query_region distance
#> ENSE00001787178   exon chr1-453633-454166 chr1-713460-714823   259293
#> ENSE00001787178.1 exon chr1-453633-454166 chr1-752422-753038   298255
#> ENSE00001787178.2 exon chr1-453633-454166 chr1-762106-763359   307939
#> ENSE00001787178.3 exon chr1-453633-454166 chr1-779589-780271   325422
#> ENSE00001787178.4 exon chr1-453633-454166 chr1-804872-805761   350705
#> ENSE00001787178.5 exon chr1-453633-454166 chr1-839520-841123   385353
# }