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| Code Block |
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| title | To plot gene level and isoform level expression for gene regucalcin |
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pdf(file="regucalcin.pdf")
mygene1 <- getGene(cuff_data,'regucalcin')
expressionBarplot(mygene1)
expressionBarplot(isoforms(mygene1))
dev.off() |
| Code Block |
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| title | To plot gene level and isoform level expression for gene Rala |
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pdf(file="rala.pdf")
mygene2 <- getGene(cuff_data, 'Rala')
expressionBarplot(mygene2)
expressionBarplot(isoforms(mygene2))
dev.off() |
Take cummeRbund for a spin...
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You may need to redo Step C) every time when you reopen an R session.
Exercise 5: Visualize the distribution of fpkm values across the two different conditions using a boxplot.
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| Expand |
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| Code Block |
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| title | One possible solution |
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| gene_diff_data <- diffData(genes(cuff_data))
sig_gene_data <- subset(gene_diff_data, (ln_fold_change > 1.52))
head(sig_gene_data)
sig_geneids <- c(sig_gene_data$gene_id)
myGenes <- getGenes(cuff_data, sig_geneids)
expressionBarplot(myGenes)
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