I have list of genes in a text file, I want to get the starting and ending bps location using biomaRt R.
You have all the tools you need in your question (gene list, get start location, biomaRt)
If you google it, the first link is what you are looking for : https://support.bioconductor.org/p/28470/
Thank you for helping
gene_names=c("CYP3A5","CYP3A4")
mart<-useDataset("hsapiens_gene_ensembl",useMart("ensembl"))
getBM(c('hgnc_symbol','chromosome_name','start_position','end_position'),filters='hgnc_symbol',values=gene_names,mart)
You're welcome. Is this solve then ?
To read a list of gene inside a file you can use :
gene_names <- scan(file = "your_file.txt", sep = "\n")
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