Another issue with lapply and BioMart

Question

I recently asked a question about lapply, but now I've changed my approach and ran into more problems I can't resolve.

This is the code I'm having issues with:

Load biomaRt

library(biomaRt)

Make the hsapiens mart

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

I then extract the human genes:

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

ensembl_gene_ID <- hsapien_PC_genes$ensembl_gene_id

Set the species vector

species <- c("mmusculus", "ggallus")

This all works as expected, I run into problems when I use lapply

all_homologues <- lapply(species, function(s) getBM(attributes = c("ensembl_gene_id", 
                                                               "external_gene_name", 
                                                               get(paste0(s, "_homolog_ensembl_gene")), 
                                                               get(paste0(s, "_homolog_associated_ensembl_gene")), 
                                                               filters = "ensembl_gene_id", 
                                                               values = c(ensembl_gene_ID), 
                                                               mart = ensembl_hsapiens)))

I get the error message:

 Error in martCheck(mart) : 
  You must provide a valid Mart object. To create a Mart object use the function: useMart.  Check ?useMart for more information.

The code works perfect like this:

all_homologues <- getBM(attributes = c("ensembl_gene_id", "external_gene_name",  
                               "mmusculus_homolog_ensembl_gene", 
                               "mmusculus_homolog_associated_gene_name"),
                           filters = "ensembl_gene_id",
                           values = c(ensembl_gene_ID),
                           mart = ensembl_hsapiens)

But I have many species, so I want to be able to use a small bit of code to extract the homologues for the species, rather than have to rewrite it all for each species.

I think I'm doing something wrong with lapply as the mart works perfectly when not using lapply.

My previous question: Issue with lapply using biomart

Answer 1

After playing around with it, I've managed to get it to work by using:

all_homologues <- lapply(species, function(s) getBM(attributes = c("ensembl_gene_id", 
                                                               "external_gene_name", 
                                                               paste0(s, c("_homolog_ensembl_gene",
                                                                           "_homolog_associated_gene_name"))),
                                                filters = "ensembl_gene_id",
                                                values = c(ensembl_gene_ID),
                                                mart = ensembl_hsapiens))

Although I'm not exactly sure why?