Comments (1)
Anthony, I created a 'dev' branch and edited the ks_enrichment.R
file to add "leading edge" functionalities. In particular,
- the
.ks_test
function now returns two extra parameters:leading_edge
andleading_hits
, with the latter a vector of positions of the hits ≤ the leading edge. - the ks plot now includes a red dashed vertical line at the leading_edge x-coordinate.
- in the
.ks_enrichment
function, thedata
table has been modified: the column 'hits' now reports the list of "genes" in the leading_hits; and the columnoverlap
now reports the number of genes in the leading edge (instead of the size of the entire set as before). Also, the function returns an extra argument,leading_hits
, a character vector of the genes in the leading edge. Right now, this is ignored by the calling function (hypeR), but perhaps worth "propagating" it up, should the user need to access that info.
I have done some perfunctory testing of those functions, and they seem to work fine. Up to you if/when to merge them to the main branch.
from hyper.
Related Issues (20)
- GSEA arguement not recognised hypeR HOT 1
- Error in conexion HOT 1
- quiet
- reactable should be "wider" HOT 1
- Enrichment maps unable to export in a .tiff format HOT 2
- Duplicated gene symbols in the output of msigdb_download HOT 6
- sizes argument in hyp_dots function HOT 1
- error in GSEA about weighted signatures HOT 1
- How to get signetures enriched in a pathway? HOT 1
- hypeR-dot plots with KS test should incorporate directionality information
- KS with mx.diff=TRUE (GSVA-like)
- .check_overlap returns a fraction, not a percentage HOT 1
- Error in hyp_hmap HOT 2
- X-axis and Outputting Gene Overlap Size HOT 2
- .kstest needs to match ks.test (modulo the sign)
- MSigDB C7 retrieval fails
- rgsets does not support proper object "duplication" by value
- Hits names should be quoted (like in the csv format)
- Pushing to upstream on Bioc
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from hyper.