suppressPackageStartupMessages({
library(AnnotationHub)
library(rtracklayer)
})
ah <- AnnotationHub()
## snapshotDate(): 2018-10-04
encode <- ah[["AH5016"]]
## downloading 0 resources
## loading from cache
## '/Users/lwaldron//.AnnotationHub/5016'
encode
## UCSC track 'encodeRegions'
## UCSCData object with 44 ranges and 1 metadata column:
## seqnames ranges strand | name
## <Rle> <IRanges> <Rle> | <character>
## [1] chr1 151158061-151658060 * | ENr231
## [2] chr2 51658705-52158704 * | ENr112
## [3] chr2 118294574-118794573 * | ENr121
## [4] chr2 220277346-220777345 * | ENr331
## [5] chr2 234491825-234991888 * | ENr131
## ... ... ... ... . ...
## [40] chr19 54331773-55332648 * | ENm007
## [41] chr20 33841513-34341514 * | ENr333
## [42] chr21 33746366-35442351 * | ENm005
## [43] chr21 40322597-40822596 * | ENr133
## [44] chr22 31803954-33503953 * | ENm004
## -------
## seqinfo: 93 sequences (1 circular) from hg19 genome
metadata(encode)
## $AnnotationHubName
## [1] "AH5016"
##
## $`File Name`
## [1] "encodeRegions"
##
## $`Data Source`
## [1] "rtracklayer://hgdownload.cse.ucsc.edu/goldenpath/hg19/database/encodeRegions"
##
## $Provider
## [1] "UCSC"
##
## $Organism
## [1] "Homo sapiens"
##
## $`Taxonomy ID`
## [1] 9606
tracks <- read.delim("~/Downloads/encodeRegions", header=FALSE)
encodemanual <- with(tracks, rtracklayer::GRangesForUCSCGenome(genome="hg19",
chrom=V1,
ranges=IRanges::IRanges(V2, V3),
names=V4))
encodemanual
## GRanges object with 44 ranges and 1 metadata column:
## seqnames ranges strand | names
## <Rle> <IRanges> <Rle> | <factor>
## [1] chr1 151158060-151658060 * | ENr231
## [2] chr10 55483812-55983812 * | ENr114
## [3] chr11 1743415-2349463 * | ENm011
## [4] chr11 4774419-5776011 * | ENm009
## [5] chr11 64184312-64684312 * | ENr332
## ... ... ... ... . ...
## [40] chr7 126078655-127241852 * | ENm014
## [41] chr8 118813039-119313039 * | ENr321
## [42] chr9 131685301-132185301 * | ENr232
## [43] chrX 122782314-123282314 * | ENr324
## [44] chrX 153114297-154409887 * | ENm006
## -------
## seqinfo: 93 sequences from hg19 genome
metadata(encodemanual)
## list()
genome(encodemanual)
## chr1 chr2 chr3
## "hg19" "hg19" "hg19"
## chr4 chr5 chr6
## "hg19" "hg19" "hg19"
## chr7 chr8 chr9
## "hg19" "hg19" "hg19"
## chr10 chr11 chr12
## "hg19" "hg19" "hg19"
## chr13 chr14 chr15
## "hg19" "hg19" "hg19"
## chr16 chr17 chr18
## "hg19" "hg19" "hg19"
## chr19 chr20 chr21
## "hg19" "hg19" "hg19"
## chr22 chrX chrY
## "hg19" "hg19" "hg19"
## chrM chr1_gl000191_random chr1_gl000192_random
## "hg19" "hg19" "hg19"
## chr4_ctg9_hap1 chr4_gl000193_random chr4_gl000194_random
## "hg19" "hg19" "hg19"
## chr6_apd_hap1 chr6_cox_hap2 chr6_dbb_hap3
## "hg19" "hg19" "hg19"
## chr6_mann_hap4 chr6_mcf_hap5 chr6_qbl_hap6
## "hg19" "hg19" "hg19"
## chr6_ssto_hap7 chr7_gl000195_random chr8_gl000196_random
## "hg19" "hg19" "hg19"
## chr8_gl000197_random chr9_gl000198_random chr9_gl000199_random
## "hg19" "hg19" "hg19"
## chr9_gl000200_random chr9_gl000201_random chr11_gl000202_random
## "hg19" "hg19" "hg19"
## chr17_ctg5_hap1 chr17_gl000203_random chr17_gl000204_random
## "hg19" "hg19" "hg19"
## chr17_gl000205_random chr17_gl000206_random chr18_gl000207_random
## "hg19" "hg19" "hg19"
## chr19_gl000208_random chr19_gl000209_random chr21_gl000210_random
## "hg19" "hg19" "hg19"
## chrUn_gl000211 chrUn_gl000212 chrUn_gl000213
## "hg19" "hg19" "hg19"
## chrUn_gl000214 chrUn_gl000215 chrUn_gl000216
## "hg19" "hg19" "hg19"
## chrUn_gl000217 chrUn_gl000218 chrUn_gl000219
## "hg19" "hg19" "hg19"
## chrUn_gl000220 chrUn_gl000221 chrUn_gl000222
## "hg19" "hg19" "hg19"
## chrUn_gl000223 chrUn_gl000224 chrUn_gl000225
## "hg19" "hg19" "hg19"
## chrUn_gl000226 chrUn_gl000227 chrUn_gl000228
## "hg19" "hg19" "hg19"
## chrUn_gl000229 chrUn_gl000230 chrUn_gl000231
## "hg19" "hg19" "hg19"
## chrUn_gl000232 chrUn_gl000233 chrUn_gl000234
## "hg19" "hg19" "hg19"
## chrUn_gl000235 chrUn_gl000236 chrUn_gl000237
## "hg19" "hg19" "hg19"
## chrUn_gl000238 chrUn_gl000239 chrUn_gl000240
## "hg19" "hg19" "hg19"
## chrUn_gl000241 chrUn_gl000242 chrUn_gl000243
## "hg19" "hg19" "hg19"
## chrUn_gl000244 chrUn_gl000245 chrUn_gl000246
## "hg19" "hg19" "hg19"
## chrUn_gl000247 chrUn_gl000248 chrUn_gl000249
## "hg19" "hg19" "hg19"