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Use latest GSVA API
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igordot committed Jan 5, 2024
1 parent 89685d4 commit 25dcc84
Showing 1 changed file with 2 additions and 2 deletions.
4 changes: 2 additions & 2 deletions R/enrichment.R
Original file line number Diff line number Diff line change
Expand Up @@ -75,14 +75,14 @@ get_scores <- function(expr_mat, markers_list, method = c("gsva", "ssgsea", "sin

if (method == "gsva" || method == "all") {
gsva_param <- GSVA::gsvaParam(exprData = expr_mat, geneSets = markers_list, kcdf = "Gaussian")
scores_mat <- GSVA::gsva(expr = gsva_param, verbose = FALSE)
scores_mat <- GSVA::gsva(gsva_param, verbose = FALSE)
scores_tbl <- lengthen_scores(scores_mat)
scores_gsva_tbl <- dplyr::select(scores_tbl, "cluster", "celltype_full", score_rank_gsva = "score_rank")
}

if (method == "ssgsea" || method == "all") {
ssgsea_param <- GSVA::ssgseaParam(exprData = expr_mat, geneSets = markers_list)
scores_mat <- GSVA::gsva(expr = ssgsea_param, verbose = FALSE)
scores_mat <- GSVA::gsva(ssgsea_param, verbose = FALSE)
scores_tbl <- lengthen_scores(scores_mat)
scores_ssgsea_tbl <- dplyr::select(scores_tbl, "cluster", "celltype_full", score_rank_ssgsea = "score_rank")
}
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