getRegionGeneAssociations-GreatObject-method.RdGet region-gene associations
# S4 method for GreatObject
getRegionGeneAssociations(object, term_id = NULL, by_middle_points = FALSE,
use_symbols = TRUE)A GreatObject-class object returned by great.
Term ID.
Whether the distances are calculated from the middle points of input regions?
Whether to use gene symbols
A GRanges object. Please the two meta columns are in formats of CharacterList
and IntegerList because a region may associate to multiple genes.
obj = readRDS(system.file("extdata", "GreatObject.rds", package = "rGREAT"))
getRegionGeneAssociations(obj)
#> GRanges object with 3716 ranges and 2 metadata columns:
#> seqnames ranges strand | annotated_genes dist_to_TSS
#> <Rle> <IRanges> <Rle> | <CharacterList> <IntegerList>
#> [1] chr1 1310673-1311002 * | AURKAIP1 0
#> [2] chr1 1342596-1342925 * | MRPL20 0
#> [3] chr1 1509774-1510103 * | SSU72 159
#> [4] chr1 1711638-1711967 * | NADK -130
#> [5] chr1 2323002-2323331 * | RER1,MORN1 0,-9
#> ... ... ... ... . ... ...
#> [3712] chr22 48494091-48494420 * | TAFA5 -390868
#> [3713] chr22 50247107-50247215 * | ZBED4 -282
#> [3714] chr22 50629956-50630285 * | TRABD,SELENOO 5597,-9123
#> [3715] chr22 50969288-50969617 * | SCO2,TYMP -4383,-774
#> [3716] chr22 50978038-50978367 * | ODF3B,KLHDC7B -7030,-8095
#> -------
#> seqinfo: 23 sequences from an unspecified genome; no seqlengths