Replace https://mygene.info golem_utils_server.R line 98 by the gene description below:
library(dplyr) library(biomaRt)
mart <- useMart('ENSEMBL_MART_ENSEMBL') mart <- useDataset('hsapiens_gene_ensembl', mart)
gff_compare <- read.table( file.path("phaseFinal/stringtie_merge/fix_comp_ref.merged_each.fix.gtf.tmap"), header = 1 ) %>% select(ref_gene_id) %>% distinct()
annotLookup <- getBM( mart = mart, attributes = c( 'ensembl_gene_id', 'gene_biotype', 'external_gene_name', 'description'), filters = 'ensembl_gene_id', values = gff_compare$ref_gene_id, uniqueRows=TRUE)
annotLookup <- annotLookup %>% mutate(description = stringr::str_remove(description, " \[[^.]*$")) saveRDS(annotLookup, 'phaseFinal/data/gene_description.RDS')