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- readCufflinks- Most important function designed to read all the output files that cuffdiff generates into an R data object (of class CuffSet).
- cuff_data <- readCufflinks(diff_out)
- CummeRbund has at least 6 classes that it will place different parts of your data in.
- Now you can access information using different functions: gene information using genes(cuff_data), your isoform level output using isoforms(cuff_data), TSS related groups using tss(cuff_data) and so forth
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