Comments (6)
By the way, the mdf
data frame can be easily converted to the list with base split
function:
mdf <- msigdbr(species, category, subcategory) %>%
dplyr::select(gs_name, gene_symbol) %>%
distinct()
gsets <- split(mdf$gene_symbol, mdf$gs_name)
Note that the gene set names will become list names automatically.
from hyper.
Thanks, good catch! Will fix ASAP. Fortunately this bug ends up getting canceled out during the enrichment steps where both the signature and genesets are reduced to unique elements.
signature <- unique(signature)
genesets <- lapply(genesets, unique)
from hyper.
Yes, it's true. The reduce method also removes duplicates.
from hyper.
What version of msigdb are you using?
My version doesn't seem to have duplicated gene symbols in any of the geneset collections I've tested.
hypeR::msigdb_version()
#> [1] "v7.2.1"
g <- hypeR::msigdb_download("Homo sapiens", category="H")
table(duplicated(g$HALLMARK_APICAL_JUNCTION))
#>
#> FALSE
#> 200
Created on 2021-08-23 by the reprex package (v2.0.0)
from hyper.
I use 7.4.1.
I believe they added Ensembl ID output in the latest version., around May this year.
from hyper.
Fixed, thank you.
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
- 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
- rctbl_build does not work with method="ks" HOT 1
- .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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