get_pathway_mat_scExp: Get pathway matrix

In vallotlab/ChromSCape: Analysis of single-cell epigenomics datasets with a Shiny App

Get pathway matrix

Description

Get pathway matrix

Usage

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
)

Arguments

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.

Value

A matrix of cell to pathway

Examples

data(scExp)
mat = get_pathway_mat_scExp(scExp, pathways = "KEGG_T_CELL_RECEPTOR_SIGNALING_PATHWAY")

vallotlab/ChromSCape documentation built on Oct. 15, 2023, 1:47 p.m.