Pathway_pcascore_run: Pathway_pcascore_run

In dengchunyu/scPagwas: A pathway-based polygenic integration method for inferring disease-associated individual cells in single cell sequencing data

Pathway_pcascore_run

Description

The function can calculate the pathway pcascore for celltypes and single cells.

Usage

Pathway_pcascore_run(
  Pagwas = NULL,
  Pathway_list = NULL,
  min.pathway.size = 10,
  max.pathway.size = 1000
)

Arguments

Pagwas	Pagwas format
Pathway_list	Pathawy gene list(gene symbol),list name is pathway name.
min.pathway.size	Threshold for min pathway gene size.
max.pathway.size	Threshold for max pathway gene size.

Value

pca score for pathway in single data and celltypes

Author(s)

Chunyu Deng

Examples

library(scPagwas)
Pagwas <- list()
# Start to read the single cell data
Single_data <- readRDS(system.file("extdata", "scRNAexample.rds",
  package = "scPagwas"
))
Pagwas <- Single_data_input(
  Pagwas = Pagwas,
  assay = "RNA",
  Single_data = Single_data,
  Pathway_list = Genes_by_pathway_kegg
)
Single_data <- Single_data[, colnames(Pagwas$data_mat)]
# Run pathway pca score!
Pagwas <- Pathway_pcascore_run(
  Pagwas = Pagwas,
  Pathway_list = Genes_by_pathway_kegg
)

dengchunyu/scPagwas documentation built on Nov. 29, 2024, 2:53 p.m.