search for: getbm

I'm using 'getBM' function in Bioconductor package 'biomaRt' to retrieve gene ids based on known chromosome locations. The question is getBM just only return one gene id once a time, even a query is mapped to multiple genes. What's the criteria for picking that special one? [[alternative HTM...

..._46", host="www.biomart.org", path="/biomart/martservice", port=80, archive=TRUE) mart<-useDataset("mmusculus_gene_ensembl", mart=mart) I'm able to list the available attributes and filters just fine, but when I attempt to actually retrieve data using getBM() I receive the following error: > genes<-getBM(attributes=c("ensembl_gene_id", "external_gene_id", "description", "chromosome_name", "start_position", "transcript_start"), + filters=c("chromosome_name","start&qu...

...'RCurl' had non-zero exit status 3: In install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, : installation of package 'biomaRt' had non-zero exit status > > library(biomaRt) Error in library(biomaRt) : there is no package called 'biomaRt' > ?getBM No matches for "getBM" have been found > ?getSequence No matches for "getSequence" have been found tutti i telefonini TIM! [[alternative HTML version deleted]]

...GGGGGAGCCGCGGGCTCTCGGGGAAGAGACGG      10644                                                          No UTR is annotated for this transcript      10644   Problem 2:Problem is here protein = getSequence(id=c(100, 5728),type="entrezgene",seqType="peptide", mart=ensembl) Error in getBM(c(seqType, type), filters = type, values = id, mart = mart,  :    Query ERROR: caught BioMart::Exception::Database: Error during query execution: Can't create/write to file '/mnt/ephemeral0/mysqltmp/#sql_40a_0.MYI' (Errcode: 2) I need help please. /.......Tanvir Ahamed [[alternative...

...the addition of data for all the other alleles of one SNP) plus a table of minor allele frequencies from each source (which would also be nice - but not necessary). Does there exist a package in R with coding which could extract the data from NCBI for all the alleles of one SNP ? I've looked at getBM() from package biomaRt and searched via Google and Copilot- so far with no success. Many thanks. remotes::install_github("ropensci/rsnps") library("rsnps") # Define the SNP ID snp_id <- "rs11134679" ## this SNP has alleles A, C, G and T, but results are only for A...

...> > >> >> > > >> mouse.homolog<-getHomolog(id =rat.entrezgene.ID, from.mart = rat.mart, >> > from.type = "entrezgene", > > + to.type="entrezgene", to.mart=mouse.mart) > > Warning message: > > getBM returns NULL. in: getHomolog(id = rat.entrezgene.ID, from.mart = > rat.mart, from.type = "entrezgene", > > > > > > >> sessionInfo() >> > > R version 2.4.1 (2006-12-18) > > i386-pc-mingw32 > > > > locale: > >...

If I run an analysis which generates statistical tests on many SNPs I would naturally want to get more details on the most significant SNPs. Directly from within R one can get the information by loading RSNPer (from Bioconductor) and simply issuing a command SNPinfo(2073285). Unfortunately, the command cannot handle a vector and therefore only wants to do one at a time. I tried the lapply and