I am using the github biomaRt version 2.37.5 am able to successful pull orthologs across a number of species. However, when I switch to trying to pull paralogs I get an curl timing out error. See the below code. I have tried different hosts. I have even limited the attributes to just "ensembl_gene_id" "hsapiens_paralog_ensembl_gene" I have also tried using the "values" parameter and limiting the number of genes to <100. It does not appear to be an actual latency or data volume issue.
Thanks for any pointers!
human <- useMart(biomart = "ENSEMBL_MART_ENSEMBL", dataset = "hsapiens_gene_ensembl", host = "useast.ensembl.org") attr <- as.data.table(listAttributes(human)) attributes <- c("ensembl_gene_id", attr[grepl("paralog", name), name]) para <- getBM(attributes, filters = "with_hsapiens_paralog", values = TRUE, mart = human)