How to get the number of exons and visualize them?

Question

[marija]

Hello everyone, I would like to ask you how can I get the number of exon? I want visualize gene length vs. number of exons in gene.

For example:

I have the length of the gene:

exons <- getBM(attributes = c("external_gene_name","start_position","end_position","ensembl_exon_id"),
          filters = "chromosome_name",
          values = "21",
          mart = genes)
exons[5] <- exons$end_position - exons$start_position
names(exons)[5] <- "gene_length"

I tried to find out the number of exons:

as.data.frame(table(exons$ensembl_exon_id))

But now, I don't know what else. Please, somebody would help me?

Answer 1

[Nicolas Rosewick]

Something like :

require(tidyverse)
genes <- useDataset("hsapiens_gene_ensembl",mart=ensembl)
exons <- getBM(attributes =
      c("external_gene_name","start_position","end_position","ensembl_exon_id"),
      filters = "chromosome_name",
      values = "21",
      mart = genes)
exons <- as.tibble(exons)
exons.plot <- exons %>% 
    mutate(len=end_position-start_position) %>% 
    group_by(external_gene_name) %>% 
    summarize(geneLen=sum(len),exonNumber=n())
# plot
ggplot(exons.plot,aes(x=geneLen,y=exonNumber))+
  geom_point(alpha=0.5)+
  scale_y_log10()+
  scale_x_log10()+
  theme_bw()

FYI you should use ensembl_gene_id instead of gene name

[marija]

@Nicolas Please do you know explain me why you use this command:

exonNumber=n()

Thank you

[Nicolas Rosewick]

n() reports the number of elements in each group thus the number of exons