I'm going through the tophat/cufflinks/cuffmerge/cuffdiff/cummeRbund protocol just published at Nature Protocols. I'm wondering how to get a different identifier (e.g. the gene symbol instead of XLOC) in the diffData(genes(cuff)) output for printing tables, annotating plots, etc.
Code:
> cuff <- readCufflinks() > gene_diff_data <- diffData(genes(cuff)) > sig_gene_data <- subset(gene_diff_data, significant=="yes") > head(sig_gene_data) gene_id sample_1 sample_2 status value_1 value_2 ln_fold_change test_stat p_value q_value significant 3 XLOC_000003 C1 C2 OK 48.7791 77.9603 0.676476 -11.81010 0.00000e+00 0.00000e+00 yes 60 XLOC_000060 C1 C2 OK 65.0337 107.4470 0.724360 -39.42460 0.00000e+00 0.00000e+00 yes 81 XLOC_000081 C1 C2 OK 26.8576 23.4374 -0.196521 4.68763 2.76389e-06 1.26818e-04 yes 175 XLOC_000175 C1 C2 OK 2724.4700 2514.0400 -0.115971 7.49516 6.61693e-14 4.70596e-12 yes 237 XLOC_000237 C1 C2 OK 23.3386 19.1596 -0.284646 3.73237 1.89689e-04 6.18840e-03 yes 250 XLOC_000250 C1 C2 OK 24.0661 42.1466 0.808413 -9.23741 0.00000e+00 0.00000e+00 yes >
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