Question

how to annotate GenomicRanges objects with genome build

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Levi Waldron ★ 1.1k

@levi-waldron-3429

Last seen 9 weeks ago

CUNY Graduate School of Public Health a…

Is there any "standard" or "recommended" way to annotate the metadata of GenomicRanges objects with the reference genome, in particular GRangesList and RangedSummarizedExperiment? I looked to parathyroidSE for an answer, and the closest I found was:

> metadata(rowRanges(parathyroidGenesSE))$genomeInfo$`BioMart dataset version` [1] "GRCh37.p11"

grangeslist rangedsummarizedexperiment parathyroidSE genomicranges granges • 1.8k views

ADD COMMENT • link 8.7 years ago Levi Waldron ★ 1.1k

score 0 · Answer 1 · 2016-03-16

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Michael Lawrence ★ 11k

@michael-lawrence-3846

Last seen 2.9 years ago

United States

Unless I misunderstand, it's just:

genome(parathyroidGenesSE) <- "GRCh37"

ADD COMMENT • link 8.7 years ago Michael Lawrence ★ 11k

score 0 · Answer 2 · 2016-03-16

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Levi Waldron ★ 1.1k

@levi-waldron-3429

Last seen 9 weeks ago

CUNY Graduate School of Public Health a…

Thanks Michael. I can for the objects I care about, although not for parathyroideGenesSE:

> library(parathyroidSE)

> data(parathyroidGenesSE)

> genome(parathyroidGenesSE) <- "GRCh37" Error in methods::slot(object, name) : no slot of name "call" for this object of class "GRangesList"

> class(parathyroidGenesSE) [1] "RangedSummarizedExperiment" attr(,"package") [1] "SummarizedExperiment"

> seqinfo(parathyroidGenesSE) Seqinfo object with 580 sequences (1 circular) from an unspecified genome: seqnames seqlengths isCircular genome 1 249250621 FALSE <NA> 2 243199373 FALSE <NA> 3 198022430 FALSE <NA> 4 191154276 FALSE <NA> 5 180915260 FALSE <NA> ... ... ... ... LRG_94 12428 FALSE <NA> LRG_96 93210 FALSE <NA> LRG_97 25996 FALSE <NA> LRG_98 18750 FALSE <NA> LRG_99 13294 FALSE <NA>

ADD COMMENT • link 8.7 years ago Levi Waldron ★ 1.1k

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Please comment rather than answer. Also, please provide sessionInfo().

ADD REPLY • link 8.7 years ago Michael Lawrence ★ 11k

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A workaround seems to be genome(rowRanges(parathyroidGenesSE)) = "GRCh37".

ADD REPLY • link 8.7 years ago Martin Morgan 25k

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Thanks for the reminder about commenting Michael, and for the workaround Martin. But FYI my `sessionInfo()` is:

> sessionInfo()
R Under development (unstable) (2016-01-30 r70052)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.10.5 (Yosemite)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] parathyroidSE_1.9.0         SummarizedExperiment_1.1.22 Biobase_2.31.3             
[4] GenomicRanges_1.23.24       GenomeInfoDb_1.7.6          IRanges_2.5.40             
[7] S4Vectors_0.9.42            BiocGenerics_0.17.3        

loaded via a namespace (and not attached):
[1] zlibbioc_1.17.0    rsconnect_0.4.1.11 XVector_0.11.7     tools_3.3.0

ADD REPLY • link 8.7 years ago Levi Waldron ★ 1.1k