Trying the gene viewer in the shiny app, it gives an error when using the ext_gene, it shows me the option but says that the object does not exist.
The Ensembl_ID works normally in the Shiny.
And I am able to plot it normally outside the shiny app, using the plot_bootstrap function.
t2g<-getBM(attributes=c('ensembl_transcript_id_version','ensembl_gene_id','external_gene_name'), mart = ensembl)
t2g <- dplyr::rename(t2g, target_id = ensembl_transcript_id_version,
ens_gene = ensembl_gene_id, ext_gene = external_gene_name
so <- sleuth_prep(s2c, target_mapping = t2g,
aggregation_column = 'ext_gene', extra_bootstrap_summary = TRUE,
read_bootstrap_tpm = TRUE, max_bootstrap = 10, gene_mode=TRUE,
transform_fun_counts= function(x) log2(x + 0.5))
so <- sleuth_fit(so, ~Cell, 'full')
so <- sleuth_fit(so, ~1, 'reduced')
so <- sleuth_lrt(so, 'reduced', 'full')
sleuth_live(so)
Listening on http://127.0.0.1:42427
Warning: Error in eval: object 'ext_gene' not found
[No stack trace available]
Hi sleuth team,
Trying the gene viewer in the shiny app, it gives an error when using the ext_gene, it shows me the option but says that the object does not exist.
The Ensembl_ID works normally in the Shiny.
And I am able to plot it normally outside the shiny app, using the plot_bootstrap function.
Any suggestions?
Am I doing something wrong?
I appreciate the help!
Thanks