BioMart: Is there a way to easily change the species for all of my code?

问题

Below is a small fraction of my code:

library(biomaRt)

ensembl_hsapiens <- useMart("ensembl", 
                        dataset = "hsapiens_gene_ensembl")

hsapien_PC_genes <- getBM(attributes = c("ensembl_gene_id", "external_gene_name"), 
                      filters = "biotype", 
                      values = "protein_coding", 
                      mart = ensembl_hsapiens)

paralogues[["hsapiens"]] <- getBM(attributes = c("external_gene_name",
                                                 "hsapiens_paralog_associated_gene_name"), 
                                  filters = "ensembl_gene_id", 
                                  values = c(ensembl_gene_ID) , mart = ensembl_hsapiens)

This bit of code will only allow me to extract the paralogues for hsapiens, it there a way for me to easily get the same information for mmusculus (mouse) and ggallus (chicken) without having to rewrite the code by using something like Tapply? My code is much longer than the snippet provided, all I would need to do is swap the word hsapiens for mmusulus and ggallus.

回答1:

Easy way is to just wrap it all in a for loop:

library(biomaRt)

species <- c("hsapiens_gene_ensembl", "mmusculus_gene_ensembl", "ggallus_gene_ensembl")

for (s in species) {
tmp <- useMart("ensembl", dataset = paste0(s))
hsapien_PC_genes <- getBM(attributes = c("ensembl_gene_id", "external_gene_name"), 
                          filters = "biotype", 
                          values = "protein_coding", 
                          mart = tmp)
paralogues[[s]] <- getBM(attributes = c("external_gene_name",
                                                 "hsapiens_paralog_associated_gene_name"), 
                                  filters = "ensembl_gene_id", 
                                  values = c(ensembl_gene_ID) , mart = tmp)
}

This should work, I haven't tested it because I don't have those packages installed. I've changed the names of some vars to make more sense (eg tmp)

来源：https://stackoverflow.com/questions/50007584/biomart-is-there-a-way-to-easily-change-the-species-for-all-of-my-code

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bioinformatics

bioconductor

biomart