Does FDR0.95 in file name really mean 95% false discovery rate?

HLee-Six / HSC_phylodynamics

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Does FDR0.95 in file name really mean 95% false discovery rate? #1

Open winni2k opened 5 years ago

winni2k commented 5 years ago

Hi, I am wondering if FDR0.95 in the file name assign_mutations_to_tree_code_and_files/Shearwater_calls_FDR0.95_all_muts.txt really means a false discovery rate of 95%? This seems high. Is this perhaps shorthand for an FDR of 5%?

winni2k commented 5 years ago

There is also this sentence in the Supplementary information:

After correcting for multiple testing with the Benjamini-Hochberg procedure, only variants were kept that were significantly mutated over the error model, using a corrected p value cutoff of 0.05.

Does this passage refer to the assign_mutations_to_tree_code_and_files/Shearwater_calls_FDR0.95_all_muts.txt file?

winni2k commented 5 years ago

Or does the passage above refer to this file instead: assign_mutations_to_tree_code_and_files/Shared_mutations.txt?