## ----setup, echo = FALSE-------------------------------------------------------------------------- knitr::opts_chunk$set(error = TRUE, cache = FALSE, eval = TRUE) options(width=100) ## ------------------------------------------------------------------------------------------------- library(biomaRt) ## ----test-wormbase-ssl, echo = FALSE-------------------------------------------------------------- if(grepl(try(httr::GET('https://parasite.wormbase.org'), silent = TRUE)[1], pattern = "sslv3 alert handshake")) { httr::set_config(httr::config(ssl_cipher_list = "DEFAULT@SECLEVEL=1")) } ## ----wormbase, echo=TRUE, eval=TRUE--------------------------------------------------------------- listMarts(host = "parasite.wormbase.org") wormbase <- useMart(biomart = "parasite_mart", host = "https://parasite.wormbase.org", port = 443) ## ----wormbase-2, echo=TRUE, eval=TRUE------------------------------------------------------------- listDatasets(wormbase) wormbase <- useDataset(mart = wormbase, dataset = "wbps_gene") head(listFilters(wormbase)) head(listAttributes(wormbase)) getBM(attributes = c("external_gene_id", "wbps_transcript_id", "transcript_biotype"), filters = "gene_name", values = c("unc-26","his-33"), mart = wormbase) ## ---- phytozome-1, echo = TRUE, eval = TRUE------------------------------------------------------- listMarts(host = "https://phytozome.jgi.doe.gov") phytozome <- useMart(biomart = "phytozome_mart", host = "https://phytozome.jgi.doe.gov") listDatasets(phytozome) phytozome <- useDataset(mart = phytozome, dataset = "phytozome") ## ---- pytozome-2---------------------------------------------------------------------------------- getBM(attributes = c("organism_name", "gene_name1"), filters = "gene_name_filter", values = "82092", mart = phytozome) ## ---- phytozome-13, echo = TRUE, eval = TRUE------------------------------------------------------ phytozome_v13 <- useMart(biomart = "phytozome_mart", dataset = "phytozome", host = "https://phytozome-next.jgi.doe.gov") ## ----sessionInfo---------------------------------------------------------------------------------- sessionInfo() warnings()