Update LinkPeaks - #1992
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- changed default peak-TSS matching strategy - added link attributes - LinkPeaks no longer runs zscore calcs by default - removed expectation for gene_biotype when using gencode annotations
Resolve conflicts in R/links.R: - keep the FindCandidateLinks-based candidate generation from this branch - carry over the v2 fixes: restrict FindTopFeatures output to count/percentile, guard against fewer than two trans peaks when computing background z-scores, and filter p-values once on the assembled links rather than inside the per-gene worker - add the missing make_empty_links() helper Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
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Thanks @JavenTyr |
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add FindCandidateLinks; mod LinkPeaks; mod CollapseToLongestTranscript
changed default peak-TSS matching strategy
added link attributes
LinkPeaks no longer runs zscore calcs by default
removed expectation for gene_biotype when using gencode annotations