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> rowData(ra)$rowanno <- LETTERS[seq_len(nrow(ra))]
> rowData(ra)
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function ‘getListElement’ for signature ‘"GRanges"’
Also, colData now returns the row annotation (??):
> colData(ra)
DataFrame with 6 rows and 1 column
rowanno
<character>
1 A
2 B
3 C
4 D
5 E
6 F
> sessionInfo()
R version 3.5.0 (2018-04-23)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.3
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
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] parallel stats4 stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] RaggedExperiment_1.5.0 GenomicRanges_1.33.1 GenomeInfoDb_1.17.0
[4] IRanges_2.15.4 S4Vectors_0.19.2 BiocGenerics_0.27.0
loaded via a namespace (and not attached):
[1] lattice_0.20-35 matrixStats_0.53.1
[3] bitops_1.0-6 grid_3.5.0
[5] zlibbioc_1.27.0 XVector_0.21.0
[7] Matrix_1.2-14 BiocParallel_1.15.0
[9] tools_3.5.0 Biobase_2.41.0
[11] RCurl_1.95-4.10 DelayedArray_0.7.0
[13] compiler_3.5.0 SummarizedExperiment_1.11.1
[15] GenomeInfoDbData_1.1.0
>
The text was updated successfully, but these errors were encountered:
Even though there is a brow, what would be the interpretation of rowRanges
for a ragged experiment? Do you have a use case?
--
Levi Waldron
http://www.waldronlab.io
Assistant Professor of Biostatistics CUNY School of Public Health
US: +1 646-364-9616 Skype:
levi.waldron
For instance, you can think of the individual CNV calls from ABSOLUTE - which would correspond to the rowRanges here.
You might want to annotate quality measures to the calls such as the number of probes supporting this call.
Hi Ludwig, @lgeistlinger
In this instance, mcols and rowData are both referring to the same information, annotations of the ranges in a GRangesList.
Essentially when you do mcols<- or rowData<-, you're adding to "number of assays". Since each column in mcols is an "assay". That's how RaggedExperiment is represented.
I found a bug in the replacement method that will fix this. Thanks!
Some arbitrary
colData
annotation:Ok.
Some arbitrary
rowData
annotation:Also,
colData
now returns the row annotation (??):The text was updated successfully, but these errors were encountered: