R API for browsing, analyzing, and manipulating reference-aligned genome graphs in a GenomicRanges framework
Home Page: http://mskilab.com/gGnome/tutorial.html
License: MIT License
Hi，
I met this error when I exactly followed the tutorial of gGnome:
svaba = jJ(system.file('extdata', "HCC1143.svaba.somatic.sv.vcf", package = "gGnome"))
gg = gG(juncs = svaba)
plot(gg$gt,'1', links = svaba$grl)
Error in as.double(x) :
cannot coerce type 'S4' to vector of type 'double'
How could I solve it?
By the way, I was also rejected by IBM to install academic CPLEX studio to JaBba. I wonder if it's a common problem for Chinese university students. Any suggestion? Or can I use the gridss-purple-linx instead of this package?
Thank you very much!!!
Hello,
I am trying to install gGnome on Windows, however I am repeatedly receiving the below error:
Error: package or namespace load failed for 'gGnome' in library.dynam(lib, package, package.lib):
DLL 'gGnome' not found: maybe not installed for this architecture?
I have followed the recommended steps in the readme, and I had a colleague successfully run the installation on Mac. I copied their steps/code, including the recommendations in issue #63 , but am still seeing this error. Is gGnome incompatible with the below architecture?
sessionInfo()
R version 4.3.1 (2023-06-16 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19045)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.utf8 LC_CTYPE=English_United States.utf8
[3] LC_MONETARY=English_United States.utf8 LC_NUMERIC=C
[5] LC_TIME=English_United States.utf8
time zone: America/Chicago
tzcode source: internal
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] gChain_0.2.0 rtracklayer_1.62.0 Matrix_1.6-5
[4] bamUtils_0.0.0.9000 gUtils_0.2.0 GenomicAlignments_1.38.2
[7] Rsamtools_2.18.0 Biostrings_2.70.2 XVector_0.42.0
[10] SummarizedExperiment_1.32.0 Biobase_2.62.0 MatrixGenerics_1.14.0
[13] matrixStats_1.2.0 GenomicRanges_1.54.1 GenomeInfoDb_1.38.6
[16] IRanges_2.36.0 S4Vectors_0.40.2 BiocGenerics_0.48.1
[19] data.table_1.15.2 ellipsis_0.3.2 testthat_3.2.1
[22] devtools_2.4.5 usethis_2.2.3
loaded via a namespace (and not attached):
[1] bitops_1.0-7 fastmap_1.1.1 RCurl_1.98-1.14 promises_1.2.1
[5] XML_3.99-0.16.1 digest_0.6.33 mime_0.12 lifecycle_1.0.4
[9] processx_3.8.3 magrittr_2.0.3 compiler_4.3.1 rlang_1.1.1
[13] tools_4.3.1 yaml_2.3.8 knitr_1.45 gTrack_0.1.0
[17] S4Arrays_1.2.1 htmlwidgets_1.6.4 pkgbuild_1.4.3 curl_5.2.1
[21] DelayedArray_0.28.0 pkgload_1.3.4 abind_1.4-5 BiocParallel_1.36.0
[25] miniUI_0.1.1.1 purrr_1.0.2 desc_1.4.3 grid_4.3.1
[29] urlchecker_1.0.1 profvis_0.3.8 xtable_1.8-4 cli_3.6.1
[33] rmarkdown_2.26 crayon_1.5.2 remotes_2.4.2.1 rstudioapi_0.15.0
[37] rjson_0.2.21 sessioninfo_1.2.2 cachem_1.0.8 stringr_1.5.1
[41] zlibbioc_1.48.0 parallel_4.3.1 BiocManager_1.30.22 restfulr_0.0.15
[45] vctrs_0.6.5 callr_3.7.5 glue_1.7.0 codetools_0.2-19
[49] ps_1.7.6 stringi_1.8.3 later_1.3.2 BiocIO_1.12.0
[53] htmltools_0.5.7 brio_1.1.4 GenomeInfoDbData_1.2.11 R6_2.5.1
[57] evaluate_0.23 shiny_1.8.0 lattice_0.22-5 memoise_2.0.1
[61] httpuv_1.6.14 Rcpp_1.0.12 SparseArray_1.2.4 xfun_0.40
[65] fs_1.6.3
I've had a great deal of issues trying to get the Rcplex running, even with the correct version of CPLEX (12.6.3) on multiple operating systems, with a great deal of changing install flags, etc. Is there some way to get some of the functionality of your package without getting Rcplex up and running?
I have some low purity FFPE samples that I have done Whole genome sequencing on and have run through jabba/ggnome. I have noted an increase in the double minutes called in these types of samples - is this an expected artifact of the poor quality sample?
Maybe I'm misunderstanding something, but in the "" section, there is the sentence:
The REF edges connecting a node to its right reference neighbor consist of two adjacencies: one leaving the “+” GRanges associated with the node and entering the “+” GRanges of its neighor...
Should that read?
The REF edges connecting a node to its right reference neighbor consist of two adjacencies: one leaving the “+” GRanges associated with the node and entering the “-” GRanges of its neighor...
(where the REF adjacency leaves the "+" side of the node, enters the "-" side of its' neighbor)
Or am I misunerstanding something?
Hi everyone.
I am running Jabba and gGnome on two breast cancer lines MCF-7 and HCC1954, starting with the bam files of CCLE consortium. The issue is that gg$edges are blank, and the events() function calls 0 type of events of known classes.
These are the commands that I am using to generate the graph :
vcf="MCF7.manta.tumor.svs.hg38.vcf"
cov="MCF7.cov.corrected.bedgraph.txt"
jba $vcf \
$cov \
-n "${vcf%%.*}" \
--cores=32
and
gg = readRDS("jabba.gg.rds")
gg$meta
gg$edges
gg$edges produces :
> head(gg$edges,2)
gEdge object with 2 edges
sedge.id cn type CHROM POS paramRangeID REF ALT QUAL FILTER IMPRECISE
1: 1 2 REF <NA> NA <NA> <NA> NA <NA> NA
2: 2 2 REF <NA> NA <NA> <NA> NA <NA> NA
SVTYPE SVLEN END CIPOS CIEND CIGAR MATEID EVENT HOMLEN HOMSEQ SVINSLEN
1: <NA> NA <NA>
2: <NA> NA <NA>
SVINSSEQ LEFT_SVINSSEQ RIGHT_SVINSSEQ BND_DEPTH MATE_BND_DEPTH mateid svtype
1: NA NA <NA>
2: NA NA <NA>
first right coord mcoord mix MATECHROM MATEPOS tier like.indel edge.id class
1: NA NA <NA> <NA> NA <NA> NA NA NA 1 REF
2: NA NA <NA> <NA> NA <NA> NA NA NA 2 REF
n1.side n2.side n1 n2
1: right left 1 2
2: right left 2 3
and no events are found (at lest simple events should have been listed) :
c = events(gg)
c$meta
$simple
Null data.table (0 rows and 0 cols)
$amp
Null data.table (0 rows and 0 cols)
$chromothripsis
Null data.table (0 rows and 0 cols)
$chromoplexy
Null data.table (0 rows and 0 cols)
$tic
Null data.table (0 rows and 0 cols)
$events
Empty data.table (0 rows and 1 cols): ev.id
The R version is :
> R.Version()
$platform
[1] "x86_64-apple-darwin17.0"
$arch
[1] "x86_64"
$os
[1] "darwin17.0"
$system
[1] "x86_64, darwin17.0"
$status
[1] ""
$major
[1] "4"
$minor
[1] "2.2"
$year
[1] "2022"
$month
[1] "10"
$day
[1] "31"
$`svn rev`
[1] "83211"
$language
[1] "R"
$version.string
[1] "R version 4.2.2 (2022-10-31)"
$nickname
[1] "Innocent and Trusting"
Hello!
When running the tool I sometimes will get complex rearrangements with CN calls like seen below which are not believable. How should these be interpreted - artifact?
Thanks,
Michael
Hi there- how can i switch the legend off ?
Or how can i reposition it ?
Appreciate that this is a random question but i've been looking around and can't find how to do it.
A
Im trying to create a gGraph using a bedpe input. However, Im getting an error that looks like a data.table error in the gG function. Thinking if bedpe format is the problem, I also ran Svaba on my sample but using this vcf did not fix my error either. Have you come across this before and if so, are there ways around it?
Thanks,
Teja
svaba = jJ("/Users/yellapav/local/downloads/R-3.5.0/I-H-135463-T1-2-D1-1.svaba.somatic.sv.vcf")
gg = gG(juncs = svaba)
Error in[.data.table(private$pedges, .(id2),:=(paste(colName), data)) :
Supplied 168 items to be assigned to 336 items of column 'class'. The RHS length must either be 1 (single values are ok) or match the LHS length exactly. If you wish to 'recycle' the RHS please use rep() explicitly to make this intent clear to readers of your code.
Since I'm working with hg38, I'd love to have a version of the http://mskilab.com/gTrack/hg19//gencode.composite.collapsed.rds file for hg38.
If there isn't already one available, how can I create one for myself (that has the same fields and organization as the one you make available?
Hi,
library("gGnome")
RDS_17_T1_31_23564<-readRDS("17_T1_31_23564.rds") ## it seems that 'readRDS()' is from gGnome package, not basic R function.
junctions=RDS_17_T1_31_23564$junctions$breakpoints
Error: Failed to install 'gGnome' from GitHub:
Failed to install 'gUtils' from GitHub:
Failed to install 'S4Vectors' from Bioc:
Could not find tools necessary to compile a package
Call pkgbuild::check_build_tools(debug = TRUE) to diagnose the problem.
Error: Failed to install 'gGnome' from GitHub:
Failed to install 'gTrack' from GitHub:
Failed to install 'rtracklayer' from Bioc:
(converted from warning) cannot remove prior installation of package ‘S4Vectors’
Another error message I got while installing gGnome;
Installing package into ‘/home/biotech/R/x86_64-pc-linux-gnu-library/4.0’
(as ‘lib’ is unspecified)
ERROR: dependencies ‘gTrack’, ‘VariantAnnotation’ are not available for package ‘gGnome’
removing ‘/home/biotech/R/x86_64-pc-linux-gnu-library/4.0/gGnome’
There were 12 warnings (use warnings() to see them)
Thank you,
Sanghoon
> library(gGnome)
> library(GenomicRanges)
> ## SvAbA
> svaba = jJ(system.file('extdata', "HCC1143.svaba.somatic.sv.vcf", package = "gGnome"))
>
> ## DELLY
> delly = jJ(system.file('extdata', "delly.final.vcf.gz", package = "gGnome"))
>
> ## novobreak
> novobreak = jJ(system.file('extdata', "novoBreak.pass.flt.vcf", package = "gGnome"))
>
> ## BEDPE
> bedpe = jJ(system.file('extdata', "junctions.bedpe", package = "gGnome"))
> head(novobreak[1:2, 1:10])
Junction Object with 2 junctions
> novobreak[ALT == "<TRA>" & QUAL>50, 1:10][1:2, 1:5]
Junction Object with 2 junctions
> svaba[nchar(INSERTION)>10, ][1:2, 1:5]
Junction Object with 2 junctions
> svaba[svaba$sign>0 & svaba$span<1e5][1:2, 1:5]
Junction Object with 2 junctions
> delly[is.infinite(delly$span) & HOMLEN>5, ][1:2,1:5]
Junction Object with 2 junctions
> svaba %&% delly
Junction Object with 7 junctions
... (3 additional junctions)
> res = merge(svaba = svaba[, c()], delly = delly[, c()],
+ novo = novobreak[, c()], anynameworks = bedpe[,c()], pad = 1e3)
> library(UpSetR)
> library(data.table)
> ## munge res$dt into upset friendly format
> df = as.data.frame(sign(as.matrix(res$dt)))
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'x' in selecting a method for function 'as.data.frame': non-numeric argument to mathematical function
> sessionInfo()
R version 4.1.1 (2021-08-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18363)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] UpSetR_1.4.0 gGnome_0.1 reshape2_1.4.4 gTrack_0.1.0 gUtils_0.2.0 GenomicRanges_1.44.0 GenomeInfoDb_1.28.4 IRanges_2.26.0
[9] S4Vectors_0.30.2 BiocGenerics_0.38.0 Matrix_1.3-4 igraph_1.2.6 data.table_1.14.2
loaded via a namespace (and not attached):
[1] bitops_1.0-7 matrixStats_0.61.0 bit64_4.0.5 filelock_1.0.2 progress_1.2.2 httr_1.4.2
[7] tools_4.1.1 utf8_1.2.2 R6_2.5.1 DBI_1.1.1 lazyeval_0.2.2 colorspace_2.0-2
[13] gridExtra_2.3 tidyselect_1.1.1 prettyunits_1.1.1 bit_4.0.4 curl_4.3.2 compiler_4.1.1
[19] cli_3.0.1 Biobase_2.52.0 xml2_1.3.2 DelayedArray_0.18.0 plotly_4.9.4.1 rtracklayer_1.52.1
[25] scales_1.1.1 rappdirs_0.3.3 stringr_1.4.0 digest_0.6.28 Rsamtools_2.8.0 XVector_0.32.0
[31] pkgconfig_2.0.3 htmltools_0.5.2 MatrixGenerics_1.4.3 BSgenome_1.60.0 dbplyr_2.1.1 fastmap_1.1.0
[37] htmlwidgets_1.5.4 rlang_0.4.11 rstudioapi_0.13 RSQLite_2.2.8 BiocIO_1.2.0 generics_0.1.0
[43] zoo_1.8-9 jsonlite_1.7.2 BiocParallel_1.26.2 dplyr_1.0.7 VariantAnnotation_1.38.0 RCurl_1.98-1.5
[49] magrittr_2.0.1 GenomeInfoDbData_1.2.6 fishHook_0.1 Rcpp_1.0.7 munsell_0.5.0 fansi_0.5.0
[55] lifecycle_1.0.1 stringi_1.7.5 yaml_2.2.1 SummarizedExperiment_1.22.0 zlibbioc_1.38.0 plyr_1.8.6
[61] BiocFileCache_2.0.0 grid_4.1.1 blob_1.2.2 crayon_1.4.1 lattice_0.20-45 Biostrings_2.60.2
[67] GenomicFeatures_1.44.2 hms_1.1.1 KEGGREST_1.32.0 knitr_1.36 pillar_1.6.3 rjson_0.2.20
[73] biomaRt_2.48.3 XML_3.99-0.8 glue_1.4.2 vctrs_0.3.8 png_0.1-7 gtable_0.3.0
[79] purrr_0.3.4 tidyr_1.1.4 assertthat_0.2.1 cachem_1.0.6 ggplot2_3.3.5 xfun_0.26
[85] restfulr_0.0.13 viridisLite_0.4.0 tibble_3.1.5 GenomicAlignments_1.28.0 AnnotationDbi_1.54.1 memoise_2.0.0
[91] ellipsis_0.3.2
PGV function returns an error if any samples in dataset have 0 junctions.
Hi,
I am using gG(jabba='file')$walks() to list walks in the cancer genome. From JaBba, we got complex graphs, e.g., thousands of nodes and edges. I filtered these nodes, but sometimes I missed some walks that I'm interested.
I tested the gG()$walks(), and found it works well for edges number less than ~ 400, but it crashes if there are more 400 edges. I noticed the greedy heuristic is not yet implemented, and am wondering when it be available, or if there are some alternative methods to exhaustively generates all walks for complex graphs.
Thanks!
Bo
Hi,
I do get the following error message while trying to install :
ERROR: dependency ‘gChain’ is not available for package ‘gGnome’
Could you please advise? I am using R version 3.6.2.
Thanks,
Breaks in the first plot example from the tutorial:
> library(gGnome)
Loading required package: data.table
data.table 1.14.0 using 36 threads (see ?getDTthreads). Latest news: r-datatable.com
Loading required package: igraph
Attaching package: ‘igraph’
The following objects are masked from ‘package:stats’:
decompose, spectrum
The following object is masked from ‘package:base’:
union
Loading required package: Matrix
Loading required package: gTrack
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:parallel’:
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from ‘package:igraph’:
normalize, path, union
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:base’:
anyDuplicated, append, as.data.frame, basename, cbind, colnames,
dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unsplit, which.max, which.min
Loading required package: S4Vectors
Attaching package: ‘S4Vectors’
The following object is masked from ‘package:Matrix’:
expand
The following objects are masked from ‘package:data.table’:
first, second
The following object is masked from ‘package:base’:
expand.grid
Loading required package: IRanges
Attaching package: ‘IRanges’
The following object is masked from ‘package:data.table’:
shift
Loading required package: GenomeInfoDb
Loading required package: gUtils
Attaching package: ‘gUtils’
The following object is masked from ‘package:Matrix’:
%&%
The following object is masked from ‘package:base’:
%o%
Attaching package: ‘gTrack’
The following object is masked from ‘package:GenomicRanges’:
seqinfo<-
The following object is masked from ‘package:GenomeInfoDb’:
seqinfo<-
Loading required package: reshape2
Attaching package: ‘reshape2’
The following objects are masked from ‘package:data.table’:
dcast, melt
Warning messages:
1: multiple methods tables found for ‘seqinfo<-’
2: replacing previous import ‘GenomicRanges::shift’ by ‘data.table::shift’ when loading ‘gGnome’
3: replacing previous import ‘GenomicRanges::score’ by ‘fishHook::score’ when loading ‘gGnome’
4: replacing previous import ‘GenomicRanges::seqinfo<-’ by ‘gTrack::seqinfo<-’ when loading ‘gGnome’
5: replacing previous import ‘Matrix::%&%’ by ‘gUtils::%&%’ when loading ‘gGnome’
6: replacing previous import ‘GenomicRanges::union’ by ‘igraph::union’ when loading ‘gGnome’
7: replacing previous import ‘data.table::melt’ by ‘reshape2::melt’ when loading ‘gGnome’
8: multiple methods tables found for ‘%&%’
> svaba = jJ(system.file('extdata', "HCC1143.svaba.somatic.sv.vcf", package = "gGnome"))
[W::bcf_hdr_check_sanity] PL should be declared as Number=G
> gg = gG(juncs = svaba)
>
> plot(gg$gt, '1', links = svaba$grl)
Error in as.double(x) :
cannot coerce type 'S4' to vector of type 'double'
I'm trying to extract the events from jabba.rds file but the function presents an error (R version 4.3.2)
Steps to reproduce the behavior:
graph <- gG(jabba="path/to/jabba.rds")evs <- events(graph, verbose = T)The function is able to go till:
Finished amp (tyfonas, dm, cpxdm, bfb)
Finished chromothripsis
Error in aggregate.formula(formula = subject.id ~ grl.id, data = m, FUN = function(x) numwin - :
argument 'x' is missing -- it has been renamed from 'formula'
In addition: There were 18 warnings (use warnings() to see them)
Going through the function dels to retrieve the deletion types, there seems to be an error in the line:
simple.dels = all.dels[!(all.dels %^% (sig %Q% (count>1))) & !(all.dels %^% (other$shadow+tile.width))]
That gives the same error:
Error in aggregate.formula(formula = subject.id ~ grl.id, data = m, FUN = function(x) numwin - : argument 'x' is missing -- it has been renamed from 'formula'
I don't know if it is a problem that I only encountered, could I get some help on this?
when I tri to install gGnome (latest version as of Jan 11, 2019), I get an error as a result of a warning message that comes up when gTrack is loaded.
> devtools::install_github('mskilab/gGnome', force=TRUE)
Downloading GitHub repo mskilab/gGnome@master
Skipping 3 packages not available: GenomicRanges, rtracklayer, VariantAnnotation
✔ checking for file ‘/tmp/RtmpFJYpuO/remotes68c72a83fa04/mskilab-gGnome-81f661e/DESCRIPTION’ ...
─ preparing ‘gGnome’:
✔ checking DESCRIPTION meta-information ...
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories
Removed empty directory ‘gGnome/inst/extdata/gTrack.js’
─ building ‘gGnome_0.1.tar.gz’
Installing package into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)
* installing *source* package ‘gGnome’ ...
** R
** inst
** byte-compile and prepare package for lazy loading
Error: package or namespace load failed for ‘gTrack’:
(converted from warning) multiple methods tables found for ‘seqinfo<-’
Error : package ‘gTrack’ could not be loaded
ERROR: lazy loading failed for package ‘gGnome’
* removing ‘/usr/local/lib/R/site-library/gGnome’
* restoring previous ‘/usr/local/lib/R/site-library/gGnome’
Error in i.p(...) :
(converted from warning) installation of package ‘/tmp/RtmpFJYpuO/file68c72afe8e0f/gGnome_0.1.tar.gz’ had non-zero exit status
Hi,
I'm trying to call complex/simple events on my Jabba results. Most of the functions work, although a handful seem to fail. Is a dependency mismatch on my end?
Versions: R 3.6.1, GenomicRanges 1.34.0, gGnome 0.1, gUtils 0.2.0
Where x is loaded directly from jabba.simple.gg.rds:
> chromothripsis(x)
Error in gr.reduce(clgr, by = "cluster") :
could not find function "gr.reduce"
> tic(x)
Error in H[!duplicated(as.matrix(H) > ZERO), ] :
invalid or not-yet-implemented 'Matrix' subsetting
> qrp(x)
Error in H[!duplicated(as.matrix(H) > ZERO), ] :
invalid or not-yet-implemented 'Matrix' subsetting
Thanks,
Will
Im trying visualise SVs identified by Svaba using Ggenome. However, I get an error when trying to read the file. The file permissions are 777 and there are lines in the file.
Anyone else had this problem?
> svaba = jJ(system.file('extdata', "I-H-135463-T1-2-D1-1.svaba.somatic.sv.vcf", package = "gGnome"))
Error in read.table(file = file, header = header, sep = sep, quote = quote, :
no lines available in input
In addition: Warning message:
In file(file, "rt") :
file("") only supports open = "w+" and open = "w+b": using the former
I'm trying to get my head around the gGnome package and got a bit stuck on the data part. It looks like gGnome usually works with SV and copy number data from remixt, jabba, etc.
Is Clone-specific data essential for building gGraphs in gGnome？Can I use my own copy number data from other tools like sclust?
Here's an example of what I have:
chr1 1 2985405 2
chr1 2985406 2998881 1
chr1 2998882 3141059 2
chr1 3141060 3151059 1
chr1 3151060 4395771 2
Would love to know if this works with gGnome. Thanks for the help!
Hi there,
What's the best way to load a hg38 -aligned vcf?
library(gGnome)
library(data.table)
library(VariantAnnotation)
library(gUtils)
library(BSgenome.Hsapiens.UCSC.hg38)
Sys.setenv(R_REMOTES_NO_ERRORS_FROM_WARNINGS = TRUE)
Sys.setenv(DEFAULT_GENOME = "BSgenome.Hsapiens.UCSC.hg38::Hsapiens")
gridss <- jJ(vcf, seqlengths = hg_seqlengths())
There were 20 warnings (use warnings() to see them)
> warnings()
Warning messages:
1: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
GRanges object contains 412 out-of-bound ranges located on sequences chr1, chr2, chr3, chr4, chr5, chr6,
chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr19, chr21, chr22, and chrX.
Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not
considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of
the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for
more information.
> hg_seqlengths()
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11
248956422 242193529 198295559 190214555 181538259 170805979 159345973 145138636 138394717 133797422 135086622
chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22
133275309 114364328 107043718 101991189 90338345 83257441 80373285 58617616 64444167 46709983 50818468
chrX chrY chrM
156040895 57227415 16569
> seqinfo(gridss)
Seqinfo object with 3366 sequences from hg19 genome:
seqnames seqlengths isCircular genome
chr1 248956422 <NA> hg19
chr2 242193529 <NA> hg19
chr3 198295559 <NA> hg19
chr4 190214555 <NA> hg19
chr5 181538259 <NA> hg19
... ... ... ...
HLA-DRB1*15:01:01:04 11056 <NA> hg19
HLA-DRB1*15:02:01 10313 <NA> hg19
HLA-DRB1*15:03:01:01 11567 <NA> hg19
HLA-DRB1*15:03:01:02 11569 <NA> hg19
HLA-DRB1*16:02:01 11005 <NA> hg19
Very weird that the genome is still labelled as hg19 even though the seqlengths entirely belong to hg38 - any thoughts?
A
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