irGSEA.subset: Subset the enrichment score matrix

In chuiqin/irGSEA: The integration of single cell rank-based gene set enrichment analysis

Subset the enrichment score matrix

Description

Subset the enrichment score matrix

Usage

irGSEA.subset(
  object = NULL,
  features = NULL,
  invert = F,
  method = c("AUCell", "UCell", "singscore", "ssgsea", "JASMINE", "viper")
)

Arguments

object	Seurat object (V4 or V5).
features	Vector. The geneset want to subset.
invert	If filp the geneset want to subset.
method	A vector. Default c("AUCell", "UCell", "singscore", "ssgsea", "JASMINE", "viper").

Value

Seurat object including score matrix.

Examples

## Not run: 
# load PBMC dataset by R package SeuratData
library(Seurat)
library(SeuratData)
# download 3k PBMCs from 10X Genomics
InstallData("pbmc3k")
library(Seurat)

library(RcppML)
library(irGSEA)
library(tidyverse)
library(clusterProfiler)
data("pbmc3k.final")
pbmc3k.final <- SeuratObject::UpdateSeuratObject(pbmc3k.final)

# download gmt file
gmt_url1 <- "https://data.broadinstitute.org/"
gmt_url2 <- "gsea-msigdb/msigdb/release/2023.2.Hs/",
gmt_url3 <- "h.all.v2023.2.Hs.symbols.gmt"
gmt_url <- paste0(gmt_url1, gmt_url2, gmt_url3)
local_gmt <- "./h.all.v2023.2.Hs.symbols.gmt"
download.file(gmt_url , local_gmt)
msigdb <- clusterProfiler::read.gmt("./h.all.v2023.2.Hs.symbols.gmt")

# convert to list[hallmarker] required by irGSEA package
msigdb$term <- factor(msigdb$term)
msigdb <- msigdb %>%
  dplyr::group_split(term, .keep = F) %>%
  purrr::map( ~.x %>% dplyr::pull(gene) %>% unique(.)) %>%
  purrr::set_names(levels(msigdb$term))

pbmc3k.final1 <- irGSEA.score(object = pbmc3k.final, assay = "RNA", slot = "data",
                              custom = T, geneset = msigdb[1:25],
                              method = c("AUCell", "UCell", "singscore", "ssgsea"),
                              kcdf = 'Gaussian')
pbmc3k.final2 <- irGSEA.score(object = pbmc3k.final, assay = "RNA", slot = "data",
                              custom = T, geneset = msigdb[26:50],
                              method = c("AUCell", "UCell", "singscore", "ssgsea"),
                              kcdf = 'Gaussian')

pbmc3k.final3 <- irGSEA.merge(object.x = pbmc3k.final1,
                              object.y = pbmc3k.final2,
                              method = c("AUCell", "UCell", "singscore", "ssgsea"),
                              overwrite = T)
pbmc3k.final4 <- irGSEA.subset(object = pbmc3k.final3,
                               features = rownames(pbmc3k.final3[["AUCell"]])[1:25],
                               method = c("AUCell", "UCell", "singscore", "ssgsea"),
                               invert = F)

## End(Not run)

chuiqin/irGSEA documentation built on July 27, 2024, 6:27 a.m.