Question: exonicParts vs. disjoinExons inconsistency in usage for DEXSeq - bug?
0
gravatar for story.benjamin
4 weeks ago by
story.benjamin10 wrote:

The current DEXSeq manual suggests using:

exonicParts = exonicParts( txdb, linked.to.single.gene.only = TRUE )

To generate an "exonic parts" feature set (GRanges object).

However, the current exonicParts call in GenomicFeatures omits a step, that was previously present for disjointExons, that determined and added the exonic_part information to the metadata of the final object.

Thus following the manual in DEXSeq using the R-centric commands does not work and results in an error:

Error in DEXSeqDataSetFromSE(SE, design = ~sample + exon + condition:exon) : make sure your SummarizedExperiment object contain the columns geneid, txname and exonic_part

dexseq • 65 views
ADD COMMENTlink modified 4 weeks ago by Hervé Pagès ♦♦ 14k • written 4 weeks ago by story.benjamin10

Here would be reproducible code:

library(GenomicRanges)
library(GenomicFeatures)
library(GenomicAlignments)

hse = makeTxDbFromBiomart( biomart="ensembl", dataset="hsapiens_gene_ensembl", host="grch37.ensembl.org" )
exonicParts = exonicParts( hse, linked.to.single.gene.only = TRUE )
bamDir = system.file( "extdata", package="parathyroidSE", mustWork=TRUE )
fls = list.files( bamDir, pattern="bam$", full=TRUE )
bamlst = BamFileList( fls, index=character(), yieldSize=100000, obeyQname=TRUE )
SE = summarizeOverlaps( exonicParts, bamlst, mode="Union", singleEnd=FALSE, ignore.strand=TRUE, inter.feature=FALSE, fragments=TRUE )
colData(SE)$condition = c("A", "A", "B")
DEXSeqDataSetFromSE( SE, design= ~ sample + exon + condition:exon )
ADD REPLYlink written 4 weeks ago by story.benjamin10

Here is a hacky fix that I came up with (stealing the code from disjointExons)... but maybe something more robust would be better.

ADD REPLYlink written 4 weeks ago by story.benjamin10
Answer: exonicParts vs. disjoinExons inconsistency in usage for DEXSeq - bug?
2
gravatar for Hervé Pagès
4 weeks ago by
Hervé Pagès ♦♦ 14k
United States
Hervé Pagès ♦♦ 14k wrote:

Hi,

Thanks for the report. The problem should be addressed in GenomicFeatures 1.36.1 (release) and 1.37.1 (devel). See this commit on GitHub for the details of the changes.

GenomicFeatures 1.36.1 and 1.37.1 should become available via BiocManager::install() in the next 24h or so.

Cheers, H.

ADD COMMENTlink written 4 weeks ago by Hervé Pagès ♦♦ 14k
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