Question: how to annotate GenomicRanges objects with genome build
0
gravatar for Levi Waldron
3.4 years ago by
Levi Waldron950
CUNY Graduate School of Public Health and Health Policy, New York, NY
Levi Waldron950 wrote:

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"

ADD COMMENTlink modified 3.4 years ago • written 3.4 years ago by Levi Waldron950
Answer: how to annotate GenomicRanges objects with genome build
0
gravatar for Michael Lawrence
3.4 years ago by
United States
Michael Lawrence11k wrote:

Unless I misunderstand, it's just:

genome(parathyroidGenesSE) <- "GRCh37"
ADD COMMENTlink written 3.4 years ago by Michael Lawrence11k
Answer: how to annotate GenomicRanges objects with genome build
0
gravatar for Levi Waldron
3.4 years ago by
Levi Waldron950
CUNY Graduate School of Public Health and Health Policy, New York, NY
Levi Waldron950 wrote:

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 COMMENTlink written 3.4 years ago by Levi Waldron950

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

 

ADD REPLYlink written 3.4 years ago by Michael Lawrence11k

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

ADD REPLYlink written 3.4 years ago by Martin Morgan ♦♦ 23k

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 REPLYlink written 3.4 years ago by Levi Waldron950
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