how to annotate GenomicRanges objects with genome build
2
0
Entering edit mode
@levi-waldron-3429
Last seen 3 days 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 • 1.0k views
ADD COMMENT
0
Entering edit mode
@michael-lawrence-3846
Last seen 8 months ago
United States

Unless I misunderstand, it's just:

genome(parathyroidGenesSE) <- "GRCh37"
ADD COMMENT
0
Entering edit mode
@levi-waldron-3429
Last seen 3 days 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
0
Entering edit mode

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

 

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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

Login before adding your answer.

Traffic: 158 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6