From 8251d53290ef7dcf7dfdc5027c86396dd6015c9e Mon Sep 17 00:00:00 2001 From: Vicente Yepez <30469316+vyepez88@users.noreply.github.com> Date: Thu, 30 Mar 2023 17:29:45 +0200 Subject: [PATCH] Update README.md --- README.md | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/README.md b/README.md index 21de3e75..ef17f68a 100644 --- a/README.md +++ b/README.md @@ -15,14 +15,15 @@ Please cite our method paper if you use it in a publication: ## What's new -FRASER 2.0, an improved version of FRASER that uses the Intron Jaccard Index as -its splice metric instead of FRASER's previous three metrics along with some other -parameter optimizations of pseudocount, filtering settings and default delta cutoff, -is now available and used by default (version 1.99.0 and above). +FRASER 2.0, an improved version of FRASER, is now available and used by default (version 1.99.0 and above). +FRASER 2.0 uses the Intron Jaccard Index as its splice metric instead of FRASER's +previous three metrics along with some other parameter optimizations of pseudocount, +filtering settings and default delta cutoff. + To change the splice metric, set `fitMetrics(fds)` to one or more of the metrics specified in `FRASER::psiTypes`. For FRASER 2.0 and the Intron Jaccard Index, the new default delta cutoff is 0.1 instead of the previous value of 0.3. When using -the 3 previous metrics, the delta cutoff should therefore be manually set to 0.3 +the 3 previous metrics, the delta cutoff should be set manually to 0.3 during results extraction, e.g. `results(fds, deltaPsiCutoff=0.3,...)`. The manuscript describing these changes in more detail will be available soon.