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How to get the number of exons and visualize them?

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?

r
• 2,853 views • link
updated by Biostar Biostar • written by marija • marija

Did you do first do:

ensembl=useMart("ensembl")
ensembl = useDataset("hsapiens_gene_ensembl",mart=ensembl)

I assume you are interested in human data?

• 0 views • link
written by GenoMax GenoMax

Yes of course:

genes <- useDataset("hsapiens_gene_ensembl",mart=ensembl)
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written by marija • marija

It looks great. I don't know tidyverse package, please could I do it something similarly also with dplyr?

• 0 views • link
written by marija • marija

marija : Please use ADD COMMENT/ADD REPLY when responding to existing posts to keep threads logically organized.

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written by GenoMax GenoMax

@genomax : better put this comment under my post as it's related to dplyr

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written by Nicolas Rosewick Nicolas Rosewick

@Nicolas: Mods can only move comments (that are not real answers) to the top post. We can't select a specific location to move them to in the thread. It is not ideal but the only option currently possible. If marija reposts under your answer then we can delete this set here.

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written by GenoMax GenoMax

Sorry. And @Nicolas thank you very much.

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written by marija • marija

Accept @Nicolas' answer (green check mark) if you are happy with it.

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written by GenoMax GenoMax

1 answer

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

enter image description here

• 0 views • link
written by Nicolas Rosewick Nicolas Rosewick

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

exonNumber=n()

Thank you

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written by marija • marija

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

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written by Nicolas Rosewick Nicolas Rosewick

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