RLab3
Kirstin Nel
2024-11-18
Installing the necessary packages
knitr::opts_chunk$set(echo = TRUE)
if (!require("BiocManager", quietly=TRUE))
install.packages("BiocManager")## Bioconductor version '3.19' is out-of-date; the current release version '3.20'
## is available with R version '4.4'; see https://bioconductor.org/installBiocManager::install("TxDb.Hsapiens.UCSC.hg19.knownGene")## Bioconductor version 3.19 (BiocManager 1.30.25), R 4.4.1 (2024-06-14)## Warning: package(s) not installed when version(s) same as or greater than current; use
## `force = TRUE` to re-install: 'TxDb.Hsapiens.UCSC.hg19.knownGene'BiocManager::install("GenomicFeatures")## Bioconductor version 3.19 (BiocManager 1.30.25), R 4.4.1 (2024-06-14)## Warning: package(s) not installed when version(s) same as or greater than current; use
## `force = TRUE` to re-install: 'GenomicFeatures'BiocManager::install("BSgenome.Hsapiens.UCSC.hg19")## Bioconductor version 3.19 (BiocManager 1.30.25), R 4.4.1 (2024-06-14)## Warning: package(s) not installed when version(s) same as or greater than current; use
## `force = TRUE` to re-install: 'BSgenome.Hsapiens.UCSC.hg19'suppressPackageStartupMessages(library(GenomicFeatures))
suppressPackageStartupMessages(library(TxDb.Hsapiens.UCSC.hg19.knownGene))
suppressPackageStartupMessages(library(BSgenome.Hsapiens.UCSC.hg19))
suppressPackageStartupMessages(library(lubridate))
suppressPackageStartupMessages(library(TxDb.Hsapiens.UCSC.hg38.knownGene))
suppressPackageStartupMessages(library(ggbio))
suppressPackageStartupMessages(library(RMariaDB))Obtaining a TxDb Object
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
hg19_txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
hg19_txdb## TxDb object:
## # Db type: TxDb
## # Supporting package: GenomicFeatures
## # Data source: UCSC
## # Genome: hg19
## # Organism: Homo sapiens
## # Taxonomy ID: 9606
## # UCSC Table: knownGene
## # Resource URL: http://genome.ucsc.edu/
## # Type of Gene ID: Entrez Gene ID
## # Full dataset: yes
## # miRBase build ID: GRCh37
## # transcript_nrow: 82960
## # exon_nrow: 289969
## # cds_nrow: 237533
## # Db created by: GenomicFeatures package from Bioconductor
## # Creation time: 2015-10-07 18:11:28 +0000 (Wed, 07 Oct 2015)
## # GenomicFeatures version at creation time: 1.21.30
## # RSQLite version at creation time: 1.0.0
## # DBSCHEMAVERSION: 1.1head(seqlevels(hg19_txdb)) ## [1] "chr1" "chr2" "chr3" "chr4" "chr5" "chr6"Overview of the TxDb Object
Pre-filtering data based on Chromosomes
seqlevels(hg19_txdb) <- "chr17"
seqinfo(hg19_txdb)## Seqinfo object with 1 sequence from hg19 genome:
## seqnames seqlengths isCircular genome
## chr17 81195210 NA hg19isActiveSeq(hg19_txdb)## chr17
## TRUERetrieving data using the select() method
keys <- c("672")
columns(hg19_txdb)## [1] "CDSCHROM" "CDSEND" "CDSID" "CDSNAME" "CDSSTART"
## [6] "CDSSTRAND" "EXONCHROM" "EXONEND" "EXONID" "EXONNAME"
## [11] "EXONRANK" "EXONSTART" "EXONSTRAND" "GENEID" "TXCHROM"
## [16] "TXEND" "TXID" "TXNAME" "TXSTART" "TXSTRAND"
## [21] "TXTYPE"keytypes(hg19_txdb)## [1] "CDSID" "CDSNAME" "EXONID" "EXONNAME" "GENEID" "TXID" "TXNAME"select(hg19_txdb, keys = keys, columns="TXNAME", keytype="GENEID")## 'select()' returned 1:many mapping between keys and columns## GENEID TXNAME
## 1 672 uc010whl.2
## 2 672 uc002icp.4
## 3 672 uc010whm.2
## 4 672 uc002icu.3
## 5 672 uc010cyx.3
## 6 672 uc002icq.3
## 7 672 uc002ict.3
## 8 672 uc010whn.2
## 9 672 uc010who.3
## 10 672 uc010whp.2
## 11 672 uc010whq.1
## 12 672 uc002idc.1
## 13 672 uc010whr.1
## 14 672 uc002idd.3
## 15 672 uc002ide.1
## 16 672 uc010cyy.1
## 17 672 uc010whs.1
## 18 672 uc010cyz.2
## 19 672 uc010cza.2
## 20 672 uc010wht.1cols <- c("TXNAME", "TXSTRAND", "TXCHROM")
select(hg19_txdb, keys=keys, columns=cols, keytype="GENEID")## 'select()' returned 1:many mapping between keys and columns## GENEID TXNAME TXCHROM TXSTRAND
## 1 672 uc010whl.2 chr17 -
## 2 672 uc002icp.4 chr17 -
## 3 672 uc010whm.2 chr17 -
## 4 672 uc002icu.3 chr17 -
## 5 672 uc010cyx.3 chr17 -
## 6 672 uc002icq.3 chr17 -
## 7 672 uc002ict.3 chr17 -
## 8 672 uc010whn.2 chr17 -
## 9 672 uc010who.3 chr17 -
## 10 672 uc010whp.2 chr17 -
## 11 672 uc010whq.1 chr17 -
## 12 672 uc002idc.1 chr17 -
## 13 672 uc010whr.1 chr17 -
## 14 672 uc002idd.3 chr17 -
## 15 672 uc002ide.1 chr17 -
## 16 672 uc010cyy.1 chr17 -
## 17 672 uc010whs.1 chr17 -
## 18 672 uc010cyz.2 chr17 -
## 19 672 uc010cza.2 chr17 -
## 20 672 uc010wht.1 chr17 -Returning GRanges objects
GR <- transcripts(hg19_txdb)
GR[1:3]## GRanges object with 3 ranges and 2 metadata columns:
## seqnames ranges strand | tx_id tx_name
## <Rle> <IRanges> <Rle> | <integer> <character>
## [1] chr17 180996-183279 + | 60101 uc021tmy.1
## [2] chr17 180996-183279 + | 60102 uc021tmz.1
## [3] chr17 260118-264457 + | 60103 uc021tna.1
## -------
## seqinfo: 1 sequence from hg19 genometx_strand <- strand(GR)
tx_strand## factor-Rle of length 4487 with 2 runs
## Lengths: 2180 2307
## Values : + -
## Levels(3): + - *sum(runLength(tx_strand))## [1] 4487length(GR)## [1] 4487GR <- transcripts(hg19_txdb, filter=list(tx_chrom = "chr17", tx_strand = "+"))
length(GR)## [1] 2180unique(strand(GR))## [1] +
## Levels: + - *PR <- promoters(hg19_txdb, upstream=2000, downstream=400)
PR## GRanges object with 4487 ranges and 2 metadata columns:
## seqnames ranges strand | tx_id tx_name
## <Rle> <IRanges> <Rle> | <integer> <character>
## uc021tmy.1 chr17 178996-181395 + | 60101 uc021tmy.1
## uc021tmz.1 chr17 178996-181395 + | 60102 uc021tmz.1
## uc021tna.1 chr17 258118-260517 + | 60103 uc021tna.1
## uc010vpz.1 chr17 261234-263633 + | 60104 uc010vpz.1
## uc002frp.3 chr17 633847-636246 + | 60105 uc002frp.3
## ... ... ... ... . ... ...
## uc002kga.3 chr17 80797532-80799931 - | 64583 uc002kga.3
## uc002kge.1 chr17 80964465-80966864 - | 64584 uc002kge.1
## uc002kgf.1 chr17 81006631-81009030 - | 64585 uc002kgf.1
## uc002kgg.1 chr17 81009287-81011686 - | 64586 uc002kgg.1
## uc021ufx.1 chr17 80907005-80909404 - | 64587 uc021ufx.1
## -------
## seqinfo: 1 sequence from hg19 genomeEX <- exons(hg19_txdb)
EX[1:22]## GRanges object with 22 ranges and 1 metadata column:
## seqnames ranges strand | exon_id
## <Rle> <IRanges> <Rle> | <integer>
## [1] chr17 180996-181508 + | 215466
## [2] chr17 180996-181512 + | 215467
## [3] chr17 181591-181657 + | 215468
## [4] chr17 182847-183279 + | 215469
## [5] chr17 260118-260437 + | 215470
## ... ... ... ... . ...
## [18] chr17 685513-685932 + | 215483
## [19] chr17 686323-686567 + | 215484
## [20] chr17 691205-691372 + | 215485
## [21] chr17 694774-695741 + | 215486
## [22] chr17 699305-701487 + | 215487
## -------
## seqinfo: 1 sequence from hg19 genomelength(EX) ## [1] 15691length(GR)## [1] 2180Working with Grouped Features
GRList <- exonsBy(hg19_txdb, by = "tx")
tx_ids <- names(GRList)
head(select(hg19_txdb, keys=tx_ids, columns="TXNAME", keytype="TXID"))## 'select()' returned 1:1 mapping between keys and columns## TXID TXNAME
## 1 60101 uc021tmy.1
## 2 60102 uc021tmz.1
## 3 60103 uc021tna.1
## 4 60104 uc010vpz.1
## 5 60105 uc002frp.3
## 6 60106 uc002frq.3Predefined grouping functions
length(intronsByTranscript(hg19_txdb))## [1] 4487length(fiveUTRsByTranscript(hg19_txdb))## [1] 3440length(threeUTRsByTranscript(hg19_txdb))## [1] 3392Getting the actual sequence data
suppressPackageStartupMessages(library(BSgenome.Hsapiens.UCSC.hg19))
genome <- BSgenome.Hsapiens.UCSC.hg19
tx_seqs1 <- extractTranscriptSeqs(genome, hg19_txdb, use.names=TRUE)
suppressWarnings(translate(tx_seqs1))## AAStringSet object of length 4487:
## width seq names
## [1] 337 LHVPTPLTAVASGQKSHRAKCC...*NWVLTAYAACWFLNKIGFLL uc021tmy.1
## [2] 339 LHVPTPLTAVASGQKSHRAKCC...KLGSYCIRCLLVSK*NWVLTI uc021tmz.1
## [3] 613 SRGGRHGDAWPWPGGPR*ESPI...EVTMGSPKRNTASFINMVLS* uc021tna.1
## [4] 543 GPQGLPPRPRGPQGLPPRPRRP...PGQLQTLWLLLCCD**TSFVL uc010vpz.1
## [5] 693 SHAAPARRPDPQPRCC*RWPGA...KKWIFKVPFNCL*TSKGLICL uc002frp.3
## ... ... ...
## [4483] 1063 T*IPPTGTAGSSFTQQA*EQVL...INSYEP*GNIKCK*T*IYVIL uc002kga.3
## [4484] 815 SAGERQRSWILMHH*G*ETAQP...LHCS*PAFTRLKFFLIKM*KA uc002kge.1
## [4485] 591 QLPE*LGLQEPATTPG*FFVFL...TVQGGGDPYYTGWNKIFKSRK uc002kgf.1
## [4486] 461 AEAAG*AEPAWAGRPRRARPCR...SSRRRRPLLHRLE*NI*IS*K uc002kgg.1
## [4487] 799 LPCNSVWREQLAGLRAPRWHCC...SGDQQGLWYKQCRLLPSLAFV uc021ufx.1cds_seqs <- extractTranscriptSeqs(Hsapiens,
cdsBy(hg19_txdb, by="tx", use.names=TRUE))
translate(cds_seqs)## AAStringSet object of length 3538:
## width seq names
## [1] 128 MVGEEGQLEEAHFRKLPTEPVS...ELTTPGVRHCRHHCRHREGH* uc021tmz.1
## [2] 424 METRGPGLAVRAESRRLVGIGP...FEGNLTPKLLHSDLAPTLLE* uc021tna.1
## [3] 258 MLLTLAGGALFFPGLFALCTWA...CLLCRKAVRLFDTPQAKKDG* uc002frp.3
## [4] 226 MLLTLAGGALFFPGLFALCTWA...CLLCRKAVRLFDTPQAKKDG* uc002frq.3
## [5] 168 MYLCEWCRTRDQNRAPSLTLRN...CLLCRKAVRLFDTPQAKKDG* uc002frr.3
## ... ... ...
## [3534] 345 MNLLPCNPHGNGLLYAGFNQDH...KGECIRDVYAQFLEMTDDKL* uc002kfq.3
## [3535] 279 MSALGSPVRAYDFLLKFLLVGD...LVRPPQSPPKNCTRNSCKIS* uc002kft.3
## [3536] 724 MSLLKERKPKKPHYIPRPPGKP...KAKLQDTARVFTLRRRARVS* uc002kga.3
## [3537] 251 MEQVQTGGLRTGSGFLTSTLHV...FEDNLRSLHLQEGQDFLHFS* uc002kgf.1
## [3538] 362 MSGAGVGGASEESQAMQAHVSI...FEDNLRSLHLQEGQDFLHFS* uc002kgg.1Plotting Transcripts of a Gene Chosen gene: BRCA1
brca1_tx <- transcriptsBy(hg19_txdb, by = "gene")[["672"]] # BRCA1 gene ID
plotRanges <- function(gr, main = "Gene Transcripts") {
plot(0, type = "n", xlim = range(start(gr), end(gr)), ylim = c(0, 2),
xlab = "Genomic Range", ylab = "", yaxt = "n", main = main)
segments(start(gr), 1, end(gr), 1, lwd = 2)
}
plotRanges(brca1_tx, main = "BRCA1 Transcripts (hg19)")
Using TxDb.Hsapiens.UCSC.hg38.knownGene
txdb <- TxDb.Hsapiens.UCSC.hg38.knownGene
seqlevels(txdb)## [1] "chr1" "chr2"
## [3] "chr3" "chr4"
## [5] "chr5" "chr6"
## [7] "chr7" "chr8"
## [9] "chr9" "chr10"
## [11] "chr11" "chr12"
## [13] "chr13" "chr14"
## [15] "chr15" "chr16"
## [17] "chr17" "chr18"
## [19] "chr19" "chr20"
## [21] "chr21" "chr22"
## [23] "chrX" "chrY"
## [25] "chrM" "chr1_GL383518v1_alt"
## [27] "chr1_GL383519v1_alt" "chr1_GL383520v2_alt"
## [29] "chr1_KI270759v1_alt" "chr1_KI270760v1_alt"
## [31] "chr1_KI270761v1_alt" "chr1_KI270762v1_alt"
## [33] "chr1_KI270763v1_alt" "chr1_KI270764v1_alt"
## [35] "chr1_KI270765v1_alt" "chr1_KI270766v1_alt"
## [37] "chr1_KI270892v1_alt" "chr2_GL383521v1_alt"
## [39] "chr2_GL383522v1_alt" "chr2_GL582966v2_alt"
## [41] "chr2_KI270767v1_alt" "chr2_KI270768v1_alt"
## [43] "chr2_KI270769v1_alt" "chr2_KI270770v1_alt"
## [45] "chr2_KI270771v1_alt" "chr2_KI270772v1_alt"
## [47] "chr2_KI270773v1_alt" "chr2_KI270774v1_alt"
## [49] "chr2_KI270775v1_alt" "chr2_KI270776v1_alt"
## [51] "chr2_KI270893v1_alt" "chr2_KI270894v1_alt"
## [53] "chr3_GL383526v1_alt" "chr3_JH636055v2_alt"
## [55] "chr3_KI270777v1_alt" "chr3_KI270778v1_alt"
## [57] "chr3_KI270779v1_alt" "chr3_KI270780v1_alt"
## [59] "chr3_KI270781v1_alt" "chr3_KI270782v1_alt"
## [61] "chr3_KI270783v1_alt" "chr3_KI270784v1_alt"
## [63] "chr3_KI270895v1_alt" "chr3_KI270924v1_alt"
## [65] "chr3_KI270934v1_alt" "chr3_KI270935v1_alt"
## [67] "chr3_KI270936v1_alt" "chr3_KI270937v1_alt"
## [69] "chr4_GL000257v2_alt" "chr4_GL383527v1_alt"
## [71] "chr4_GL383528v1_alt" "chr4_KI270785v1_alt"
## [73] "chr4_KI270786v1_alt" "chr4_KI270787v1_alt"
## [75] "chr4_KI270788v1_alt" "chr4_KI270789v1_alt"
## [77] "chr4_KI270790v1_alt" "chr4_KI270896v1_alt"
## [79] "chr4_KI270925v1_alt" "chr5_GL339449v2_alt"
## [81] "chr5_GL383530v1_alt" "chr5_GL383531v1_alt"
## [83] "chr5_GL383532v1_alt" "chr5_GL949742v1_alt"
## [85] "chr5_KI270791v1_alt" "chr5_KI270792v1_alt"
## [87] "chr5_KI270793v1_alt" "chr5_KI270794v1_alt"
## [89] "chr5_KI270795v1_alt" "chr5_KI270796v1_alt"
## [91] "chr5_KI270897v1_alt" "chr5_KI270898v1_alt"
## [93] "chr6_GL000250v2_alt" "chr6_GL000251v2_alt"
## [95] "chr6_GL000252v2_alt" "chr6_GL000253v2_alt"
## [97] "chr6_GL000254v2_alt" "chr6_GL000255v2_alt"
## [99] "chr6_GL000256v2_alt" "chr6_GL383533v1_alt"
## [101] "chr6_KB021644v2_alt" "chr6_KI270758v1_alt"
## [103] "chr6_KI270797v1_alt" "chr6_KI270798v1_alt"
## [105] "chr6_KI270799v1_alt" "chr6_KI270800v1_alt"
## [107] "chr6_KI270801v1_alt" "chr6_KI270802v1_alt"
## [109] "chr7_GL383534v2_alt" "chr7_KI270803v1_alt"
## [111] "chr7_KI270804v1_alt" "chr7_KI270805v1_alt"
## [113] "chr7_KI270806v1_alt" "chr7_KI270807v1_alt"
## [115] "chr7_KI270808v1_alt" "chr7_KI270809v1_alt"
## [117] "chr7_KI270899v1_alt" "chr8_KI270810v1_alt"
## [119] "chr8_KI270811v1_alt" "chr8_KI270812v1_alt"
## [121] "chr8_KI270813v1_alt" "chr8_KI270814v1_alt"
## [123] "chr8_KI270815v1_alt" "chr8_KI270816v1_alt"
## [125] "chr8_KI270817v1_alt" "chr8_KI270818v1_alt"
## [127] "chr8_KI270819v1_alt" "chr8_KI270820v1_alt"
## [129] "chr8_KI270821v1_alt" "chr8_KI270822v1_alt"
## [131] "chr8_KI270900v1_alt" "chr8_KI270901v1_alt"
## [133] "chr8_KI270926v1_alt" "chr9_GL383539v1_alt"
## [135] "chr9_GL383540v1_alt" "chr9_GL383541v1_alt"
## [137] "chr9_GL383542v1_alt" "chr9_KI270823v1_alt"
## [139] "chr10_GL383545v1_alt" "chr10_GL383546v1_alt"
## [141] "chr10_KI270824v1_alt" "chr10_KI270825v1_alt"
## [143] "chr11_GL383547v1_alt" "chr11_JH159136v1_alt"
## [145] "chr11_JH159137v1_alt" "chr11_KI270826v1_alt"
## [147] "chr11_KI270827v1_alt" "chr11_KI270829v1_alt"
## [149] "chr11_KI270830v1_alt" "chr11_KI270831v1_alt"
## [151] "chr11_KI270832v1_alt" "chr11_KI270902v1_alt"
## [153] "chr11_KI270903v1_alt" "chr11_KI270927v1_alt"
## [155] "chr12_GL383549v1_alt" "chr12_GL383550v2_alt"
## [157] "chr12_GL383551v1_alt" "chr12_GL383552v1_alt"
## [159] "chr12_GL383553v2_alt" "chr12_GL877875v1_alt"
## [161] "chr12_GL877876v1_alt" "chr12_KI270833v1_alt"
## [163] "chr12_KI270834v1_alt" "chr12_KI270835v1_alt"
## [165] "chr12_KI270836v1_alt" "chr12_KI270837v1_alt"
## [167] "chr12_KI270904v1_alt" "chr13_KI270838v1_alt"
## [169] "chr13_KI270839v1_alt" "chr13_KI270840v1_alt"
## [171] "chr13_KI270841v1_alt" "chr13_KI270842v1_alt"
## [173] "chr13_KI270843v1_alt" "chr14_KI270844v1_alt"
## [175] "chr14_KI270845v1_alt" "chr14_KI270846v1_alt"
## [177] "chr14_KI270847v1_alt" "chr15_GL383554v1_alt"
## [179] "chr15_GL383555v2_alt" "chr15_KI270848v1_alt"
## [181] "chr15_KI270849v1_alt" "chr15_KI270850v1_alt"
## [183] "chr15_KI270851v1_alt" "chr15_KI270852v1_alt"
## [185] "chr15_KI270905v1_alt" "chr15_KI270906v1_alt"
## [187] "chr16_GL383556v1_alt" "chr16_GL383557v1_alt"
## [189] "chr16_KI270853v1_alt" "chr16_KI270854v1_alt"
## [191] "chr16_KI270855v1_alt" "chr16_KI270856v1_alt"
## [193] "chr17_GL000258v2_alt" "chr17_GL383563v3_alt"
## [195] "chr17_GL383564v2_alt" "chr17_GL383565v1_alt"
## [197] "chr17_GL383566v1_alt" "chr17_JH159146v1_alt"
## [199] "chr17_JH159147v1_alt" "chr17_JH159148v1_alt"
## [201] "chr17_KI270857v1_alt" "chr17_KI270858v1_alt"
## [203] "chr17_KI270859v1_alt" "chr17_KI270860v1_alt"
## [205] "chr17_KI270861v1_alt" "chr17_KI270862v1_alt"
## [207] "chr17_KI270907v1_alt" "chr17_KI270908v1_alt"
## [209] "chr17_KI270909v1_alt" "chr17_KI270910v1_alt"
## [211] "chr18_GL383567v1_alt" "chr18_GL383568v1_alt"
## [213] "chr18_GL383569v1_alt" "chr18_GL383570v1_alt"
## [215] "chr18_GL383571v1_alt" "chr18_GL383572v1_alt"
## [217] "chr18_KI270863v1_alt" "chr18_KI270864v1_alt"
## [219] "chr18_KI270911v1_alt" "chr18_KI270912v1_alt"
## [221] "chr19_GL000209v2_alt" "chr19_GL383573v1_alt"
## [223] "chr19_GL383574v1_alt" "chr19_GL383575v2_alt"
## [225] "chr19_GL383576v1_alt" "chr19_GL949746v1_alt"
## [227] "chr19_GL949747v2_alt" "chr19_GL949748v2_alt"
## [229] "chr19_GL949749v2_alt" "chr19_GL949750v2_alt"
## [231] "chr19_GL949751v2_alt" "chr19_GL949752v1_alt"
## [233] "chr19_GL949753v2_alt" "chr19_KI270865v1_alt"
## [235] "chr19_KI270866v1_alt" "chr19_KI270867v1_alt"
## [237] "chr19_KI270868v1_alt" "chr19_KI270882v1_alt"
## [239] "chr19_KI270883v1_alt" "chr19_KI270884v1_alt"
## [241] "chr19_KI270885v1_alt" "chr19_KI270886v1_alt"
## [243] "chr19_KI270887v1_alt" "chr19_KI270888v1_alt"
## [245] "chr19_KI270889v1_alt" "chr19_KI270890v1_alt"
## [247] "chr19_KI270891v1_alt" "chr19_KI270914v1_alt"
## [249] "chr19_KI270915v1_alt" "chr19_KI270916v1_alt"
## [251] "chr19_KI270917v1_alt" "chr19_KI270918v1_alt"
## [253] "chr19_KI270919v1_alt" "chr19_KI270920v1_alt"
## [255] "chr19_KI270921v1_alt" "chr19_KI270922v1_alt"
## [257] "chr19_KI270923v1_alt" "chr19_KI270929v1_alt"
## [259] "chr19_KI270930v1_alt" "chr19_KI270931v1_alt"
## [261] "chr19_KI270932v1_alt" "chr19_KI270933v1_alt"
## [263] "chr19_KI270938v1_alt" "chr20_GL383577v2_alt"
## [265] "chr20_KI270869v1_alt" "chr20_KI270870v1_alt"
## [267] "chr20_KI270871v1_alt" "chr21_GL383578v2_alt"
## [269] "chr21_GL383579v2_alt" "chr21_GL383580v2_alt"
## [271] "chr21_GL383581v2_alt" "chr21_KI270872v1_alt"
## [273] "chr21_KI270873v1_alt" "chr21_KI270874v1_alt"
## [275] "chr22_GL383582v2_alt" "chr22_GL383583v2_alt"
## [277] "chr22_KB663609v1_alt" "chr22_KI270875v1_alt"
## [279] "chr22_KI270876v1_alt" "chr22_KI270877v1_alt"
## [281] "chr22_KI270878v1_alt" "chr22_KI270879v1_alt"
## [283] "chr22_KI270928v1_alt" "chrX_KI270880v1_alt"
## [285] "chrX_KI270881v1_alt" "chrX_KI270913v1_alt"
## [287] "chr1_KI270706v1_random" "chr1_KI270707v1_random"
## [289] "chr1_KI270708v1_random" "chr1_KI270709v1_random"
## [291] "chr1_KI270710v1_random" "chr1_KI270711v1_random"
## [293] "chr1_KI270712v1_random" "chr1_KI270713v1_random"
## [295] "chr1_KI270714v1_random" "chr2_KI270715v1_random"
## [297] "chr2_KI270716v1_random" "chr3_GL000221v1_random"
## [299] "chr4_GL000008v2_random" "chr5_GL000208v1_random"
## [301] "chr9_KI270717v1_random" "chr9_KI270718v1_random"
## [303] "chr9_KI270719v1_random" "chr9_KI270720v1_random"
## [305] "chr11_KI270721v1_random" "chr14_GL000009v2_random"
## [307] "chr14_GL000194v1_random" "chr14_GL000225v1_random"
## [309] "chr14_KI270722v1_random" "chr14_KI270723v1_random"
## [311] "chr14_KI270724v1_random" "chr14_KI270725v1_random"
## [313] "chr14_KI270726v1_random" "chr15_KI270727v1_random"
## [315] "chr16_KI270728v1_random" "chr17_GL000205v2_random"
## [317] "chr17_KI270729v1_random" "chr17_KI270730v1_random"
## [319] "chr22_KI270731v1_random" "chr22_KI270732v1_random"
## [321] "chr22_KI270733v1_random" "chr22_KI270734v1_random"
## [323] "chr22_KI270735v1_random" "chr22_KI270736v1_random"
## [325] "chr22_KI270737v1_random" "chr22_KI270738v1_random"
## [327] "chr22_KI270739v1_random" "chrY_KI270740v1_random"
## [329] "chrUn_GL000195v1" "chrUn_GL000213v1"
## [331] "chrUn_GL000214v1" "chrUn_GL000216v2"
## [333] "chrUn_GL000218v1" "chrUn_GL000219v1"
## [335] "chrUn_GL000220v1" "chrUn_GL000224v1"
## [337] "chrUn_GL000226v1" "chrUn_KI270302v1"
## [339] "chrUn_KI270303v1" "chrUn_KI270304v1"
## [341] "chrUn_KI270305v1" "chrUn_KI270310v1"
## [343] "chrUn_KI270311v1" "chrUn_KI270312v1"
## [345] "chrUn_KI270315v1" "chrUn_KI270316v1"
## [347] "chrUn_KI270317v1" "chrUn_KI270320v1"
## [349] "chrUn_KI270322v1" "chrUn_KI270329v1"
## [351] "chrUn_KI270330v1" "chrUn_KI270333v1"
## [353] "chrUn_KI270334v1" "chrUn_KI270335v1"
## [355] "chrUn_KI270336v1" "chrUn_KI270337v1"
## [357] "chrUn_KI270338v1" "chrUn_KI270340v1"
## [359] "chrUn_KI270362v1" "chrUn_KI270363v1"
## [361] "chrUn_KI270364v1" "chrUn_KI270366v1"
## [363] "chrUn_KI270371v1" "chrUn_KI270372v1"
## [365] "chrUn_KI270373v1" "chrUn_KI270374v1"
## [367] "chrUn_KI270375v1" "chrUn_KI270376v1"
## [369] "chrUn_KI270378v1" "chrUn_KI270379v1"
## [371] "chrUn_KI270381v1" "chrUn_KI270382v1"
## [373] "chrUn_KI270383v1" "chrUn_KI270384v1"
## [375] "chrUn_KI270385v1" "chrUn_KI270386v1"
## [377] "chrUn_KI270387v1" "chrUn_KI270388v1"
## [379] "chrUn_KI270389v1" "chrUn_KI270390v1"
## [381] "chrUn_KI270391v1" "chrUn_KI270392v1"
## [383] "chrUn_KI270393v1" "chrUn_KI270394v1"
## [385] "chrUn_KI270395v1" "chrUn_KI270396v1"
## [387] "chrUn_KI270411v1" "chrUn_KI270412v1"
## [389] "chrUn_KI270414v1" "chrUn_KI270417v1"
## [391] "chrUn_KI270418v1" "chrUn_KI270419v1"
## [393] "chrUn_KI270420v1" "chrUn_KI270422v1"
## [395] "chrUn_KI270423v1" "chrUn_KI270424v1"
## [397] "chrUn_KI270425v1" "chrUn_KI270429v1"
## [399] "chrUn_KI270435v1" "chrUn_KI270438v1"
## [401] "chrUn_KI270442v1" "chrUn_KI270448v1"
## [403] "chrUn_KI270465v1" "chrUn_KI270466v1"
## [405] "chrUn_KI270467v1" "chrUn_KI270468v1"
## [407] "chrUn_KI270507v1" "chrUn_KI270508v1"
## [409] "chrUn_KI270509v1" "chrUn_KI270510v1"
## [411] "chrUn_KI270511v1" "chrUn_KI270512v1"
## [413] "chrUn_KI270515v1" "chrUn_KI270516v1"
## [415] "chrUn_KI270517v1" "chrUn_KI270518v1"
## [417] "chrUn_KI270519v1" "chrUn_KI270521v1"
## [419] "chrUn_KI270522v1" "chrUn_KI270528v1"
## [421] "chrUn_KI270529v1" "chrUn_KI270530v1"
## [423] "chrUn_KI270538v1" "chrUn_KI270539v1"
## [425] "chrUn_KI270544v1" "chrUn_KI270548v1"
## [427] "chrUn_KI270579v1" "chrUn_KI270580v1"
## [429] "chrUn_KI270581v1" "chrUn_KI270582v1"
## [431] "chrUn_KI270583v1" "chrUn_KI270584v1"
## [433] "chrUn_KI270587v1" "chrUn_KI270588v1"
## [435] "chrUn_KI270589v1" "chrUn_KI270590v1"
## [437] "chrUn_KI270591v1" "chrUn_KI270593v1"
## [439] "chrUn_KI270741v1" "chrUn_KI270742v1"
## [441] "chrUn_KI270743v1" "chrUn_KI270744v1"
## [443] "chrUn_KI270745v1" "chrUn_KI270746v1"
## [445] "chrUn_KI270747v1" "chrUn_KI270748v1"
## [447] "chrUn_KI270749v1" "chrUn_KI270750v1"
## [449] "chrUn_KI270751v1" "chrUn_KI270752v1"
## [451] "chrUn_KI270753v1" "chrUn_KI270754v1"
## [453] "chrUn_KI270755v1" "chrUn_KI270756v1"
## [455] "chrUn_KI270757v1" "chr1_KN196472v1_fix"
## [457] "chr1_KN196473v1_fix" "chr1_KN196474v1_fix"
## [459] "chr1_KN538360v1_fix" "chr1_KN538361v1_fix"
## [461] "chr1_KQ031383v1_fix" "chr1_KZ208906v1_fix"
## [463] "chr1_KZ559100v1_fix" "chr1_MU273333v1_fix"
## [465] "chr1_MU273334v1_fix" "chr1_MU273335v1_fix"
## [467] "chr1_MU273336v1_fix" "chr2_KN538362v1_fix"
## [469] "chr2_KN538363v1_fix" "chr2_KQ031384v1_fix"
## [471] "chr2_ML143341v1_fix" "chr2_ML143342v1_fix"
## [473] "chr2_MU273341v1_fix" "chr2_MU273342v1_fix"
## [475] "chr2_MU273343v1_fix" "chr2_MU273344v1_fix"
## [477] "chr2_MU273345v1_fix" "chr3_KN196475v1_fix"
## [479] "chr3_KN196476v1_fix" "chr3_KN538364v1_fix"
## [481] "chr3_KQ031385v1_fix" "chr3_KQ031386v1_fix"
## [483] "chr3_KV766192v1_fix" "chr3_KZ559104v1_fix"
## [485] "chr3_MU273346v1_fix" "chr3_MU273347v1_fix"
## [487] "chr3_MU273348v1_fix" "chr4_KQ983257v1_fix"
## [489] "chr4_ML143344v1_fix" "chr4_ML143345v1_fix"
## [491] "chr4_ML143346v1_fix" "chr4_ML143347v1_fix"
## [493] "chr4_ML143348v1_fix" "chr4_ML143349v1_fix"
## [495] "chr4_MU273350v1_fix" "chr4_MU273351v1_fix"
## [497] "chr5_KV575244v1_fix" "chr5_ML143350v1_fix"
## [499] "chr5_MU273352v1_fix" "chr5_MU273353v1_fix"
## [501] "chr5_MU273354v1_fix" "chr5_MU273355v1_fix"
## [503] "chr6_KN196478v1_fix" "chr6_KQ031387v1_fix"
## [505] "chr6_KQ090016v1_fix" "chr6_KV766194v1_fix"
## [507] "chr6_KZ208911v1_fix" "chr6_ML143351v1_fix"
## [509] "chr7_KQ031388v1_fix" "chr7_KV880764v1_fix"
## [511] "chr7_KV880765v1_fix" "chr7_KZ208912v1_fix"
## [513] "chr7_ML143352v1_fix" "chr8_KV880766v1_fix"
## [515] "chr8_KV880767v1_fix" "chr8_KZ208914v1_fix"
## [517] "chr8_KZ208915v1_fix" "chr8_MU273359v1_fix"
## [519] "chr8_MU273360v1_fix" "chr8_MU273361v1_fix"
## [521] "chr8_MU273362v1_fix" "chr8_MU273363v1_fix"
## [523] "chr9_KN196479v1_fix" "chr9_ML143353v1_fix"
## [525] "chr9_MU273364v1_fix" "chr9_MU273365v1_fix"
## [527] "chr9_MU273366v1_fix" "chr10_KN196480v1_fix"
## [529] "chr10_KN538365v1_fix" "chr10_KN538366v1_fix"
## [531] "chr10_KN538367v1_fix" "chr10_KQ090021v1_fix"
## [533] "chr10_ML143354v1_fix" "chr10_ML143355v1_fix"
## [535] "chr10_MU273367v1_fix" "chr11_KN196481v1_fix"
## [537] "chr11_KQ090022v1_fix" "chr11_KQ759759v1_fix"
## [539] "chr11_KQ759759v2_fix" "chr11_KV766195v1_fix"
## [541] "chr11_KZ559108v1_fix" "chr11_KZ559109v1_fix"
## [543] "chr11_ML143356v1_fix" "chr11_ML143357v1_fix"
## [545] "chr11_ML143358v1_fix" "chr11_ML143359v1_fix"
## [547] "chr11_ML143360v1_fix" "chr11_MU273369v1_fix"
## [549] "chr11_MU273370v1_fix" "chr11_MU273371v1_fix"
## [551] "chr12_KN196482v1_fix" "chr12_KN538369v1_fix"
## [553] "chr12_KN538370v1_fix" "chr12_KQ759760v1_fix"
## [555] "chr12_KZ208916v1_fix" "chr12_KZ208917v1_fix"
## [557] "chr12_ML143361v1_fix" "chr12_ML143362v1_fix"
## [559] "chr12_MU273372v1_fix" "chr13_KN196483v1_fix"
## [561] "chr13_KN538371v1_fix" "chr13_KN538372v1_fix"
## [563] "chr13_KN538373v1_fix" "chr13_ML143363v1_fix"
## [565] "chr13_ML143364v1_fix" "chr13_ML143365v1_fix"
## [567] "chr13_ML143366v1_fix" "chr14_KZ208920v1_fix"
## [569] "chr14_ML143367v1_fix" "chr14_MU273373v1_fix"
## [571] "chr15_KN538374v1_fix" "chr15_ML143369v1_fix"
## [573] "chr15_ML143370v1_fix" "chr15_ML143371v1_fix"
## [575] "chr15_ML143372v1_fix" "chr15_MU273374v1_fix"
## [577] "chr16_KV880768v1_fix" "chr16_KZ559113v1_fix"
## [579] "chr16_ML143373v1_fix" "chr16_MU273376v1_fix"
## [581] "chr16_MU273377v1_fix" "chr17_KV575245v1_fix"
## [583] "chr17_KV766196v1_fix" "chr17_ML143374v1_fix"
## [585] "chr17_ML143375v1_fix" "chr17_MU273379v1_fix"
## [587] "chr17_MU273380v1_fix" "chr17_MU273381v1_fix"
## [589] "chr17_MU273382v1_fix" "chr17_MU273383v1_fix"
## [591] "chr18_KQ090028v1_fix" "chr18_KZ208922v1_fix"
## [593] "chr18_KZ559115v1_fix" "chr19_KN196484v1_fix"
## [595] "chr19_KQ458386v1_fix" "chr19_ML143376v1_fix"
## [597] "chr19_MU273384v1_fix" "chr19_MU273385v1_fix"
## [599] "chr19_MU273386v1_fix" "chr20_MU273388v1_fix"
## [601] "chr20_MU273389v1_fix" "chr21_ML143377v1_fix"
## [603] "chr21_MU273390v1_fix" "chr21_MU273391v1_fix"
## [605] "chr21_MU273392v1_fix" "chr22_KQ759762v1_fix"
## [607] "chr22_KQ759762v2_fix" "chr22_ML143378v1_fix"
## [609] "chr22_ML143379v1_fix" "chr22_ML143380v1_fix"
## [611] "chrX_ML143381v1_fix" "chrX_ML143382v1_fix"
## [613] "chrX_ML143383v1_fix" "chrX_ML143384v1_fix"
## [615] "chrX_ML143385v1_fix" "chrX_MU273393v1_fix"
## [617] "chrX_MU273394v1_fix" "chrY_KN196487v1_fix"
## [619] "chrY_KZ208923v1_fix" "chrY_KZ208924v1_fix"
## [621] "chrY_MU273398v1_fix" "chr1_KQ458382v1_alt"
## [623] "chr1_KQ458383v1_alt" "chr1_KQ458384v1_alt"
## [625] "chr1_KQ983255v1_alt" "chr1_KV880763v1_alt"
## [627] "chr1_KZ208904v1_alt" "chr1_KZ208905v1_alt"
## [629] "chr1_MU273330v1_alt" "chr1_MU273331v1_alt"
## [631] "chr1_MU273332v1_alt" "chr2_KQ983256v1_alt"
## [633] "chr2_KZ208907v1_alt" "chr2_KZ208908v1_alt"
## [635] "chr2_MU273337v1_alt" "chr2_MU273338v1_alt"
## [637] "chr2_MU273339v1_alt" "chr2_MU273340v1_alt"
## [639] "chr3_KZ208909v1_alt" "chr3_KZ559101v1_alt"
## [641] "chr3_KZ559102v1_alt" "chr3_KZ559103v1_alt"
## [643] "chr3_KZ559105v1_alt" "chr3_ML143343v1_alt"
## [645] "chr4_KQ090013v1_alt" "chr4_KQ090014v1_alt"
## [647] "chr4_KQ090015v1_alt" "chr4_KQ983258v1_alt"
## [649] "chr4_KV766193v1_alt" "chr4_MU273349v1_alt"
## [651] "chr5_KN196477v1_alt" "chr5_KV575243v1_alt"
## [653] "chr5_KZ208910v1_alt" "chr5_MU273356v1_alt"
## [655] "chr6_KQ090017v1_alt" "chr6_MU273357v1_alt"
## [657] "chr7_KZ208913v1_alt" "chr7_KZ559106v1_alt"
## [659] "chr7_MU273358v1_alt" "chr8_KZ559107v1_alt"
## [661] "chr9_KQ090018v1_alt" "chr9_KQ090019v1_alt"
## [663] "chr10_KQ090020v1_alt" "chr11_KN538368v1_alt"
## [665] "chr11_KZ559110v1_alt" "chr11_KZ559111v1_alt"
## [667] "chr11_MU273368v1_alt" "chr12_KQ090023v1_alt"
## [669] "chr12_KZ208918v1_alt" "chr12_KZ559112v1_alt"
## [671] "chr13_KQ090024v1_alt" "chr13_KQ090025v1_alt"
## [673] "chr14_KZ208919v1_alt" "chr14_ML143368v1_alt"
## [675] "chr15_KQ031389v1_alt" "chr15_MU273375v1_alt"
## [677] "chr16_KQ031390v1_alt" "chr16_KQ090026v1_alt"
## [679] "chr16_KQ090027v1_alt" "chr16_KZ208921v1_alt"
## [681] "chr17_KV766197v1_alt" "chr17_KV766198v1_alt"
## [683] "chr17_KZ559114v1_alt" "chr17_MU273378v1_alt"
## [685] "chr18_KQ458385v1_alt" "chr18_KZ559116v1_alt"
## [687] "chr19_KV575246v1_alt" "chr19_KV575247v1_alt"
## [689] "chr19_KV575248v1_alt" "chr19_KV575249v1_alt"
## [691] "chr19_KV575250v1_alt" "chr19_KV575251v1_alt"
## [693] "chr19_KV575252v1_alt" "chr19_KV575253v1_alt"
## [695] "chr19_KV575254v1_alt" "chr19_KV575255v1_alt"
## [697] "chr19_KV575256v1_alt" "chr19_KV575257v1_alt"
## [699] "chr19_KV575258v1_alt" "chr19_KV575259v1_alt"
## [701] "chr19_KV575260v1_alt" "chr19_MU273387v1_alt"
## [703] "chr22_KN196485v1_alt" "chr22_KN196486v1_alt"
## [705] "chr22_KQ458387v1_alt" "chr22_KQ458388v1_alt"
## [707] "chr22_KQ759761v1_alt" "chrX_KV766199v1_alt"
## [709] "chrX_MU273395v1_alt" "chrX_MU273396v1_alt"
## [711] "chrX_MU273397v1_alt"Visualizing Transcripts with ggbio Plot Transcripts of the BRCA1 gene
# Subset for a specific transcript of the BRCA1 gene
gr <- subset(transcripts(txdb), tx_name == "ENST00000357654.9")
# Create the plot
p <- autoplot(txdb,
which = gr,
geom = "full",
coord = "genome",
layout = "linear")## Parsing transcripts...## Parsing exons...## Parsing cds...## Parsing utrs...## ------exons...## ------cdss...## ------introns...## ------utr...## aggregating...## Done## Constructing graphics...## Warning in (function (mapping = NULL, data = NULL, stat = "identity", position
## = "identity", : Ignoring unknown parameters: `coord` and `layout`## Warning in (function (mapping = NULL, data = NULL, stat = "identity", position
## = "identity", : Ignoring unknown parameters: `coord` and `layout`## Warning in (function (mapping = NULL, data = NULL, stat = "identity", position
## = "identity", : Ignoring unknown parameters: `coord` and `layout`## Warning in (function (mapping = NULL, data = NULL, stat = "identity", position
## = "identity", : Ignoring unknown parameters: `coord` and `layout`## Warning in (function (mapping = NULL, data = NULL, stat = "identity", position
## = "identity", : Ignoring unknown parameters: `coord` and `layout`## Warning in (function (mapping = NULL, data = NULL, stat = "identity", position
## = "identity", : Ignoring unknown parameters: `coord` and `layout`## Warning in (function (mapping = NULL, data = NULL, stat = "identity", position
## = "identity", : Ignoring unknown parameters: `coord` and `layout`## Warning in (function (mapping = NULL, data = NULL, stat = "identity", position
## = "identity", : Ignoring unknown parameters: `coord` and `layout`p
Explore Available Transcript IDs
all_transcripts <- transcripts(txdb)
head(all_transcripts$tx_name)## [1] "ENST00000456328.2" "ENST00000450305.2" "ENST00000473358.1"
## [4] "ENST00000469289.1" "ENST00000607096.1" "ENST00000606857.1"DEADplot
brca1 <- subset(transcripts(txdb), tx_name == "ENST00000357654.9")
print(brca1)## GRanges object with 1 range and 2 metadata columns:
## seqnames ranges strand | tx_id tx_name
## <Rle> <IRanges> <Rle> | <integer> <character>
## [1] chr17 43044295-43125364 - | 206113 ENST00000357654.9
## -------
## seqinfo: 711 sequences (1 circular) from hg38 genomebrca1plot <- autoplot(txdb,
which = brca1,
geom = "full",
coord = "genome",
layout = "linear")## Parsing transcripts...## Parsing exons...## Parsing cds...## Parsing utrs...## ------exons...## ------cdss...## ------introns...## ------utr...## aggregating...## Done## Constructing graphics...## Warning in (function (mapping = NULL, data = NULL, stat = "identity", position
## = "identity", : Ignoring unknown parameters: `coord` and `layout`## Warning in (function (mapping = NULL, data = NULL, stat = "identity", position
## = "identity", : Ignoring unknown parameters: `coord` and `layout`## Warning in (function (mapping = NULL, data = NULL, stat = "identity", position
## = "identity", : Ignoring unknown parameters: `coord` and `layout`## Warning in (function (mapping = NULL, data = NULL, stat = "identity", position
## = "identity", : Ignoring unknown parameters: `coord` and `layout`## Warning in (function (mapping = NULL, data = NULL, stat = "identity", position
## = "identity", : Ignoring unknown parameters: `coord` and `layout`## Warning in (function (mapping = NULL, data = NULL, stat = "identity", position
## = "identity", : Ignoring unknown parameters: `coord` and `layout`## Warning in (function (mapping = NULL, data = NULL, stat = "identity", position
## = "identity", : Ignoring unknown parameters: `coord` and `layout`## Warning in (function (mapping = NULL, data = NULL, stat = "identity", position
## = "identity", : Ignoring unknown parameters: `coord` and `layout`brca1plot