Closed jorainer closed 7 years ago
Thank you for heads up, @jotsetung! I'll adress this early next week at the latest.
I'll have to wait anyway for the AnnotationFilter
to be accepted (hope that this happens any day now). I'll let you know before I push the changes. In case I could also fork chimeraviz
, fix it and make a pull request.
@stianlagstad , AnnotationFilter
package is now in Bioc devel. You can go now ahead and import the GeneIdFilter
from AnnotationFilter
instead of ensembldb
. I'll push to ensembldb
tomorrow.
Is there a difference in how I use the filter? I changed my code to use AnnotationFilter::GeneIdFilter
instead of ensembldb::GeneidFilter
, but that's giving me Error in checkFilter(filter) : One of more elements in 'filter' are not filter objects!
.
The line I changed: https://github.com/stianlagstad/chimeraviz/blob/master/R/utilities.R#L558
I also tried changing it to this:
# Get all exon information
allTranscripts <- ensembldb::exonsBy(
edb,
filter = AnnotationFilter::AnnotationFilter(~ gene_id %in% c(fusion@geneA@ensemblId, fusion@geneB@ensemblId)),
columns = c(
"gene_id",
"gene_name",
"tx_id",
"tx_cds_seq_start",
"tx_cds_seq_end",
"exon_id"))
But that got me Error in checkFilter(filter) : 'filter' has to be a filter object or a list of filter objects!
.
Edit: I just realized that this might be because ensembldb
might not be updated yet :)
Yes, that might be an explanation. You can update ensembldb
from github:
library(devtools)
install_github("jotsetung/ensembldb")
@stianlagstad please replace GeneidFilter
with GeneIdFilter
(note the capital I
in Id). In AnnotationFilter
we tried to streamline all filter class names, such that filtering on a column named gene_id
is done using an GeneIdFilter
, i.e. capitalizing each character after a _
.
Thanks again, @jotsetung. I'm looking at this tonight, as my dependencies are building again today.
The filter classes will move from the
ensembldb
package to a new packageAnnotationFilter
(https://github.com/Bioconductor/AnnotationFilter). This package is not yet in Bioconductor, but once it is (hopefully soon) I will remove the filter classes from theensembldb
package.I checked your package and all you will have to do seems to be to inport the
GeneIdFilter
(has been renamed fromGeneidFilter
) fromAnnotationFilter
instead.There will also be the possibility to do the filtering with
filter = ~ gene_id == "BCL2"
instead of explicitly create a filter object.Let me know if you run into problems or need help. I'll let you know once I've removed the filter classes from
ensembldb
(eventually already this week).