I am trying to count the number of paralogues for the mouse homologues of the human protein-coding genes using BioMart. But for example in the 'PLIN4' gene its counting 35,000 paralogues instead of 4. 

We think it is because some genes have one to many paralogues which causes repeats. When I run a single gene its gives me back the correct number of paralogues. Is there a way to either remove these repeats from the results or a way around this so that BioMart doesn't output these repeats. 

I have also thought of maybe running one gene at a time, then counting it by setting up some sort of loop so that it does all of the genes from the list automatically. 

The code I have written so far is:

    # Load the biomaRt package:

    library(biomaRt)
    ensembl_hsapiens <- useMart("ensembl", 
                              dataset = "hsapiens_gene_ensembl")
    ensembl_mouse <- useMart("ensembl", 
                           dataset = "mmusculus_gene_ensembl")

    # Get all human protein coding 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

    # Get mouse homologues

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

    # Get mouse external gene name 
  
    mouse_homologues_external_gene_names <- mouse_homologues$mmusculus_homolog_associated_gene_name

    mouse_paralogues <- getBM(attributes = c("hsapiens_homolog_associated_gene_name",
                                           "external_gene_name",
                                           "mmusculus_paralog_associated_gene_name"), 
                            filters = "external_gene_name", 
                            values = c(mouse_homologues_external_gene_names) , mart = ensembl_mouse)

    # Remove genes with no paralogues 
    mouse_paralogs_data <- mouse_paralogues[!(is.na(mouse_paralogues$mmusculus_paralog_associated_gene_name)
                                              | 
    mouse_paralogues$mmusculus_paralog_associated_gene_name==""), ]

    # Count paralogues per gene
  
    library(plyr)
    count_mouse_paralogues <- count(mouse_paralogs_data, "external_gene_name")
    View(count_mouse_paralogues)

Hope someone can help

Thanks 

Jack