getRegionGeneAssociations-GreatJob-method.RdGet region-gene associations
# S4 method for GreatJob
getRegionGeneAssociations(object, ontology = NULL, term_id = NULL,
request_interval = 10, max_tries = 100, verbose = great_opt$verbose)A GreatJob-class object returned by submitGreatJob.
ontology name
Term id in the selected ontology.
Time interval for two requests. Default is 300 seconds.
Maximal times for automatically reconnecting GREAT web server.
Whether to show messages.
A GRanges object. Please the two meta columns are in formats of CharacterList
and IntegerList because a region may associate to multiple genes.
Please note, the distance is from the middle points of input regions to TSS.
job = readRDS(system.file("extdata", "GreatJob.rds", package = "rGREAT"))
gr = getRegionGeneAssociations(job)
gr
#> GRanges object with 885 ranges and 2 metadata columns:
#> seqnames ranges strand | annotated_genes dist_to_TSS
#> <Rle> <IRanges> <Rle> | <CharacterList> <IntegerList>
#> [1] chr1 9204434-9208784 * | H6PD,GPR157 -88225,-17380
#> [2] chr1 9853594-9859363 * | CLSTN1,PIK3CD 28106,144675
#> [3] chr1 10862809-10871681 * | TARDBP,CASZ1 -205454,-10540
#> [4] chr1 12716970-12723206 * | AADACL3,AADACL4 -56058,15522
#> [5] chr1 13814692-13823250 * | LRRC38,PRAMEF20 21572,82064
#> ... ... ... ... . ... ...
#> [881] chrY 16384799-16389852 * | NLGN4Y,VCY1B -248301,219228
#> [882] chrY 16842593-16846893 * | NLGN4Y 209117
#> [883] chrY 16998750-17003225 * | NLGN4Y 365361
#> [884] chrY 24401612-24406252 * | RBMY1J,RBMY1F -145685,-74837
#> [885] chrY 26206997-26215445 * | BPY2B,CDY1B -552930,-17105
#> -------
#> seqinfo: 24 sequences from an unspecified genome; no seqlengths