Skip to content

Update utils.R #159

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
ncborcherding merged 2 commits into from
Jun 3, 2025
Merged

Update utils.R #159

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
edd3d63
Update utils.R
toobiwankenobi Jun 3, 2025
65ec228
Adding Tobias as contributor
ncborcherding Jun 3, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
1 change: 1 addition & 0 deletions DESCRIPTION
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,7 @@ Version: 2.5.3
Authors@R: c(
person(given = "Nick", family = "Borcherding", role = c("aut", "cre"), email = "ncborch@gmail.com"),
person(given = "Jared", family = "Andrews", role = c("aut"), email = "jared.andrews07@gmail.com"),
person(given = "Tobias", family = "Hoch", role = c("ctb"), email = "tobias@hoch.earth"),
person(given = "Alexei", family = "Martsinkovskiy", role = c("ctb"), email = "alexei.martsinkovskiy@gmail.com")
)
Description: A bridging R package to facilitate gene set enrichment analysis (GSEA) in the context of single-cell RNA sequencing. Using raw count information, Seurat objects, or SingleCellExperiment format, users can perform and visualize ssGSEA, GSVA, AUCell, and UCell-based enrichment calculations across individual cells. Alternatively, escape supports use of rank-based GSEA, such as the use of differential gene expression via fgsea.
Expand Down
10 changes: 5 additions & 5 deletions R/utils.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -57,7 +57,7 @@
df <- cbind(value = cnts[gene.set, ], meta)
colnames(df)[1] <- gene.set
} else {
df <- cbind(t(cnts[gene.set, , drop = FALSE]), meta)
df <- cbind(Matrix::t(cnts[gene.set, , drop = FALSE]), meta)
}
df
}
Expand Down Expand Up @@ -194,7 +194,7 @@
SeuratObject::CreateAssayObject
}
suppressWarnings(
sc[[name]] <- fn(data = as.matrix(t(enrichment)))
sc[[name]] <- fn(data = as.matrix(Matrix::t(enrichment)))
)
} else {
warning("SeuratObject package is required to add enrichment to Seurat object.")
Expand All @@ -204,7 +204,7 @@
if (requireNamespace("SummarizedExperiment", quietly = TRUE) &&
requireNamespace("SingleCellExperiment", quietly = TRUE)) {
alt <- SummarizedExperiment::SummarizedExperiment(
assays = list(data = t(enrichment))
assays = list(data = Matrix::t(enrichment))
)
SingleCellExperiment::altExp(sc, name) <- alt
} else {
Expand All @@ -226,7 +226,7 @@
} else if (.is_sce(sc)) {
if (requireNamespace("SummarizedExperiment", quietly = TRUE) &&
requireNamespace("SingleCellExperiment", quietly = TRUE)) {
t(SummarizedExperiment::assay(SingleCellExperiment::altExp(sc)[[name]]))
Matrix::t(SummarizedExperiment::assay(SingleCellExperiment::altExp(sc)[[name]]))
} else {
stop("SummarizedExperiment and SingleCellExperiment packages are required to pull enrichment from SCE object.")
}
Expand Down Expand Up @@ -342,7 +342,7 @@
},
"UCELL" = {
.load_backend("UCell")
t(UCell::ScoreSignatures_UCell(matrix = expr,
Matrix::t(UCell::ScoreSignatures_UCell(matrix = expr,
features = gene_sets,
name = NULL,
BPPARAM = BPPARAM,
Expand Down