## ----setup, echo = FALSE-------------------------------------------------------------------------- knitr::opts_chunk$set(error = TRUE, cache = FALSE, eval = TRUE) ## ----annotate,echo=FALSE-------------------------------------------------------------------------- options(width=100) ## ----biomaRt-------------------------------------------------------------------------------------- library("biomaRt") listMarts() ## ----ensembl1------------------------------------------------------------------------------------- ensembl <- useMart("ensembl") ## ----listDatasets--------------------------------------------------------------------------------- datasets <- listDatasets(ensembl) head(datasets) ## ----ensembl2, eval=TRUE-------------------------------------------------------------------------- ensembl = useDataset("hsapiens_gene_ensembl",mart=ensembl) ## ----ensembl3------------------------------------------------------------------------------------- ensembl = useMart("ensembl",dataset="hsapiens_gene_ensembl") ## ----filters-------------------------------------------------------------------------------------- filters = listFilters(ensembl) filters[1:5,] ## ----attributes----------------------------------------------------------------------------------- attributes = listAttributes(ensembl) attributes[1:5,] ## ----getBM1, echo=TRUE, eval=TRUE----------------------------------------------------------------- affyids=c("202763_at","209310_s_at","207500_at") getBM(attributes=c('affy_hg_u133_plus_2', 'entrezgene_id'), filters = 'affy_hg_u133_plus_2', values = affyids, mart = ensembl) ## ----searchDatasets, echo = TRUE, eval = TRUE----------------------------------------------------- searchDatasets(mart = ensembl, pattern = "hsapiens") ## ----searchAttributes, echo = TRUE, eval = TRUE--------------------------------------------------- searchAttributes(mart = ensembl, pattern = "hgnc") ## ----searchFilters, echo = TRUE, eval = TRUE------------------------------------------------------ searchFilters(mart = ensembl, pattern = "ensembl.*id") ## ----filtervalues, fig.cap='The options available to the Chromosome/Scaffold field are limited to a pretermined list based on the values in this dataset.', echo = FALSE---- knitr::include_graphics('filtervalues.png') ## ----chromosomeNames, results = FALSE------------------------------------------------------------- listFilterValues(mart = ensembl, filter = "chromosome_name") ## ----searchFilterValues, results = FALSE---------------------------------------------------------- searchFilterValues(mart = ensembl, filter = "chromosome_name", pattern = "^GL") searchFilterValues(mart = ensembl, filter = "phenotype_description", pattern = "Crohn") ## ----attributePages------------------------------------------------------------------------------- pages = attributePages(ensembl) pages ## ----listAttributes------------------------------------------------------------------------------- head(listAttributes(ensembl, page="feature_page")) ## ----cacheInfo------------------------------------------------------------------------------------ biomartCacheInfo() ## ----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) wormbase <- 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") ## ----localCopy, eval = FALSE---------------------------------------------------------------------- # listMarts(host="www.myLocalHost.org", path="/myPathToWebservice/martservice") # mart=useMart("nameOfMyMart",dataset="nameOfMyDataset",host="www.myLocalHost.org", path="/myPathToWebservice/martservice") ## ----columnsAndKeyTypes--------------------------------------------------------------------------- mart <- useMart(dataset="hsapiens_gene_ensembl",biomart='ensembl') head(keytypes(mart), n=3) head(columns(mart), n=3) ## ----keys1---------------------------------------------------------------------------------------- k = keys(mart, keytype="chromosome_name") head(k, n=3) ## ----keys2---------------------------------------------------------------------------------------- k = keys(mart, keytype="chromosome_name", pattern="LRG") head(k, n=3) ## ----select--------------------------------------------------------------------------------------- affy=c("202763_at","209310_s_at","207500_at") select(mart, keys=affy, columns=c('affy_hg_u133_plus_2','entrezgene_id'), keytype='affy_hg_u133_plus_2') ## ----putenv, eval = FALSE------------------------------------------------------------------------- # Sys.setenv("http_proxy" = "http://my.proxy.org:9999") ## ----rCurlOptions, eval = FALSE------------------------------------------------------------------- # options(RCurlOptions = list(proxy="uscache.kcc.com:80",proxyuserpwd="------:-------")) ## ----sessionInfo---------------------------------------------------------------------------------- sessionInfo() warnings()