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Tuxedo_step_18

The code above can also be modified to write out small files containing only the differentially expressed genes. These files may be more manageable for some spreadsheet software than the full output files produced by Cuffdiff. The R snippet below writes a table of differentially expressed genes into a file named diff_genes.txt.


> gene_diff_data <- diffData(genes(cuff_data))
> sig_gene_data <- subset(gene_diff_data, (sgnificant == 'yes'))
> sig_gene_data <- subset(gene_diff_data, (significant == 'yes'))
> write.table(sig_gene_data, 'my_rnaseq_exp/diff_genes.txt', sep='\t', row.names = F, col.names = T, quote = F)
>

Categories: Bioinformatics, Tuxedo

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