View source: R/diff_analysis_gene_set_enrichment.R
get_pathway_mat_scExp | R Documentation |
Get pathway matrix
get_pathway_mat_scExp(
scExp,
pathways,
max_distanceToTSS = 1000,
ref = "hg38",
GeneSetClasses = c("c1_positional", "c2_curated", "c3_motif", "c4_computational",
"c5_GO", "c6_oncogenic", "c7_immunologic", "hallmark"),
progress = NULL
)
scExp |
A SingleCellExperiment |
pathways |
A character vector specifying the pathways to retrieve the cell count for. |
max_distanceToTSS |
Numeric. Maximum distance to a gene's TSS to consider a region linked to a gene. (1000)#' @param ref |
ref |
Reference genome, either mm10 or hg38 |
GeneSetClasses |
Which classes of MSIGdb to load |
progress |
A shiny Progress instance to display progress bar. |
A matrix of cell to pathway
data(scExp)
mat = get_pathway_mat_scExp(scExp, pathways = "KEGG_T_CELL_RECEPTOR_SIGNALING_PATHWAY")
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