Thanks Hervé and others for looking into this.
Leonard
On Sun, Oct 29, 2017 at 10:19 PM, Hervé Pagès wrote:
> Thanks Dario and Mike for looking into this.
>
> In the mean time I added makeTxDbFromEnsembl() for creating a TxDb
> object by querying directly an Ensembl MySQL server. Only lightly
>
Thanks Dario and Mike for looking into this.
In the mean time I added makeTxDbFromEnsembl() for creating a TxDb
object by querying directly an Ensembl MySQL server. Only lightly
tested but so far seems to faster and more reliable than
makeTxDbFromBiomart():
> library(GenomicFeatures)
> syst
My feeling is that this isn't related to RCurl, since the example
transcript is missing if you use httr to submit the query instead. You can
check this with the code at
https://gist.github.com/grimbough/7e7a47b7a4f64915220ce35cc1ce8f39
I wonder if this is related to BioMart's instability when yo
Good day,
I stepped through the code until execution reached the end of postForm in RCurl
which is called by getBM and obtains the textual result from the server. If I
check the contents of write$value(), the example missing transcript is not
there.
Browse[3]> grep("ENST0485971", write$val
The problem seems to originate in the BioMart service itself:
library(biomaRt)
mart <- useMart(biomart="ensembl", dataset="hsapiens_gene_ensembl")
attributes1 <- c("ensembl_transcript_id", "ensembl_exon_id")
df1 <- getBM(attributes1, mart=mart)
dim(df1)
# [1] 1150974 2
subs
Hi Leonard,
Sorry for missing your earlier posts about this. Will look into it.
Thanks,
H.
On 10/27/2017 09:07 AM, Leonard Goldstein wrote:
Dear bioc-devel,
I noticed exonsBy is dropping a lot of genes when run on a TxDb object
created with makeTxDbFromBiomart (see below). Please also see rel
Dear bioc-devel,
I noticed exonsBy is dropping a lot of genes when run on a TxDb object
created with makeTxDbFromBiomart (see below). Please also see related post
on the Bioconductor support site:
https://support.bioconductor.org/p/101951/#102160
Thanks for your help.
Leonard
--
> tx <- makeTx
