UCSC.utils 1.3.0
UCSC.utils is an infrastructure package that provides a small set of low-level utilities to retrieve data from the UCSC Genome Browser. Most functions in the package access the data via the UCSC REST API but some of them query the UCSC MySQL server directly.
Note that the primary purpose of the package is to support higher-level functionalities implemented in downstream packages like GenomeInfoDb or txdbmaker.
Like any other Bioconductor package, UCSC.utils should always
be installed with BiocManager::install():
if (!require("BiocManager", quietly=TRUE))
install.packages("BiocManager")
BiocManager::install("UCSC.utils")However, note that UCSC.utils will typically get automatically installed as a dependency of other Bioconductor packages, so explicit installation of the package is usually not needed.
suppressPackageStartupMessages(library(UCSC.utils))
list_UCSC_genomes("cat")## organism genome common_name tax_id
## 1 Felis catus felCat3 Cat 9685
## 2 Felis catus felCat4 Cat 9685
## 3 Felis catus felCat5 Cat 9685
## 4 Felis catus felCat8 Cat 9685
## 5 Felis catus felCat9 Cat 9685
## 6 Tursiops truncatus turTru2 Dolphin 9739
## description
## 1 Mar. 2006 (Broad/felCat3)
## 2 Dec. 2008 (NHGRI/GTB V17e/felCat4)
## 3 Sep. 2011 (ICGSC Felis_catus 6.2/felCat5)
## 4 Nov. 2014 (ICGSC Felis_catus_8.0/felCat8)
## 5 Nov. 2017 (Felis_catus_9.0/felCat9)
## 6 Oct. 2011 (Baylor Ttru_1.4/turTru2)See ?list_UCSC_genomes for more information and additional examples.
felCat9_chrom_sizes <- get_UCSC_chrom_sizes("felCat9")
head(felCat9_chrom_sizes)## chrA1 chrUn_NW_019369707v1 chrUn_NW_019369340v1
## 242100913 1969 2790
## chrUn_NW_019367154v1 chrUn_NW_019366602v1 chrUn_NW_019367170v1
## 2807 2835 2909See ?get_UCSC_chrom_sizes for more information and additional examples.
list_UCSC_tracks("felCat9", group="varRep")## track primary_table type group composite_track
## 1 EVA SNP Release 6 evaSnp6 bigBed 9 + varRep EVA SNP
## 2 EVA SNP Release 5 evaSnp5 bigBed 9 + varRep EVA SNP
## 3 EVA SNP Release 4 evaSnp4 bigBed 9 + varRep EVA SNP
## 4 EVA SNP Release 3 evaSnp bigBed 9 + varRep EVA SNP
## 5 Microsatellite microsat bed 4 varRep <NA>
## 6 Interrupted Rpts nestedRepeats bed 12 + varRep <NA>
## 7 RepeatMasker rmsk rmsk varRep <NA>
## 8 Simple Repeats simpleRepeat bed 4 + varRep <NA>
## 9 WM + SDust windowmaskerSdust bed 3 varRep <NA>See ?list_UCSC_tracks for more information and
additional examples.
mm9_cytoBandIdeo <- fetch_UCSC_track_data("mm9", "cytoBandIdeo")
head(mm9_cytoBandIdeo)## chrom chromStart chromEnd name gieStain
## 1 chr1 0 8918386 qA1 gpos100
## 2 chr1 8918386 12386647 qA2 gneg
## 3 chr1 12386647 20314102 qA3 gpos33
## 4 chr1 20314102 22295965 qA4 gneg
## 5 chr1 22295965 31214352 qA5 gpos100
## 6 chr1 31214352 43601000 qB gnegSee ?fetch_UCSC_track_data for more information and
additional examples.
Retrieve a full SQL table:
felCat9_refGene <- UCSC_dbselect("felCat9", "refGene")
head(felCat9_refGene)## bin name chrom strand txStart txEnd cdsStart cdsEnd
## 1 863 NM_001009849 chrE2 + 36523718 36526085 36523718 36526085
## 2 1227 NM_001009828 chrD1 - 84257818 84258562 84257818 84258562
## 3 762 NM_001009827 chrE1 - 23276059 23282999 23276460 23282943
## 4 1577 NM_001009826 chrC1 - 130088795 130092596 130089335 130092527
## 5 759 NM_001309049 chrA1 + 22918805 22920344 22919057 22920092
## 6 875 NM_001042567 chrB1 - 38074338 38098460 38074369 38098430
## exonCount exonStarts exonEnds score name2 cdsStartStat cdsEndStat
## 1 3 36523718.... 36523788.... 0 CCL17 cmpl cmpl
## 2 1 84257818 84258562 0 BDNF cmpl cmpl
## 3 4 23276059.... 23276485.... 0 CCL5 cmpl cmpl
## 4 2 13008879.... 13009038.... 0 CXCR4 cmpl cmpl
## 5 1 22918805 22920344 0 LPAR6 cmpl cmpl
## 6 10 38074338.... 38074370.... 0 LPL cmpl cmpl
## exonFrames
## 1 0, 1, 2
## 2 0
## 3 2, 2, 1, 0
## 4 0, 0
## 5 0
## 6 2, 2, 2,....Or retrieve a subset of it:
columns <- c("chrom", "strand", "txStart", "txEnd", "exonCount", "name2")
UCSC_dbselect("felCat9", "refGene", columns=columns, where="chrom='chrA1'")## chrom strand txStart txEnd exonCount name2
## 1 chrA1 + 141539866 141571963 14 HEXB
## 2 chrA1 - 138510635 138551376 10 SMN
## 3 chrA1 - 145138360 145306338 8 ARSB
## 4 chrA1 + 175374295 175382370 14 F12
## 5 chrA1 + 191099915 191109377 6 IL12B
## 6 chrA1 + 199096975 199126348 22 CSF1R
## 7 chrA1 + 11563271 11622511 32 BRCA2
## 8 chrA1 + 22918805 22920344 1 LPAR6
## 9 chrA1 - 24436704 24481859 9 LRCH1
## 10 chrA1 - 77088366 77130144 5 EFNB2
## 11 chrA1 + 82349957 82367091 9 LAMP1
## 12 chrA1 + 91725271 91726174 1 FELCATV1R2
## 13 chrA1 + 111190386 111192290 4 CSF2
## 14 chrA1 + 111190386 111192290 4 CSF2
## 15 chrA1 - 111639220 111641240 4 IL5
## 16 chrA1 + 111778711 111787544 4 IL4
## 17 chrA1 - 111946494 111949509 2 GDF9
## 18 chrA1 - 121247112 121356809 8 NR3C1
## 19 chrA1 - 161161087 161213837 6 LIX1
## 20 chrA1 + 193037229 193057081 8 HAVCR1
## 21 chrA1 - 200182785 200184042 1 ADRB2
## 22 chrA1 + 214528332 214560411 7 SLC45A2Note that UCSC_dbselect is an alternative to fetch_UCSC_track_data
that is more efficient and gives the user more control on what data to
retrieve exactly from the server. However, the downside of it is that
it does not work with all tracks!
See ?UCSC_dbselect for more information and additional examples.
sessionInfo()## R Under development (unstable) (2024-10-21 r87258)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.1 LTS
##
## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.21-bioc/R/lib/libRblas.so
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0
##
## locale:
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## [3] LC_TIME=en_GB LC_COLLATE=C
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
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## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## time zone: America/New_York
## tzcode source: system (glibc)
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] UCSC.utils_1.3.0 BiocStyle_2.35.0
##
## loaded via a namespace (and not attached):
## [1] vctrs_0.6.5 httr_1.4.7 cli_3.6.3
## [4] knitr_1.48 rlang_1.1.4 xfun_0.48
## [7] DBI_1.2.3 generics_0.1.3 jsonlite_1.8.9
## [10] bit_4.5.0 S4Vectors_0.45.0 htmltools_0.5.8.1
## [13] sass_0.4.9 stats4_4.5.0 hms_1.1.3
## [16] rmarkdown_2.28 evaluate_1.0.1 jquerylib_0.1.4
## [19] fastmap_1.2.0 yaml_2.3.10 lifecycle_1.0.4
## [22] bookdown_0.41 BiocManager_1.30.25 RMariaDB_1.3.2
## [25] compiler_4.5.0 blob_1.2.4 timechange_0.3.0
## [28] pkgconfig_2.0.3 digest_0.6.37 R6_2.5.1
## [31] curl_5.2.3 bslib_0.8.0 bit64_4.5.2
## [34] tools_4.5.0 lubridate_1.9.3 BiocGenerics_0.53.0
## [37] cachem_1.1.0