Single_data_input: Single_data_input

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

Single_data_input

Description

Input the Single data in seruat format

Usage

Single_data_input(
  Pagwas,
  Single_data,
  nfeatures = NULL,
  Pathway_list = NULL,
  assay = "RNA",
  min_clustercells = 5
)

Arguments

Pagwas	Pagwas format
Single_data	Input the Single data in seruat format, Idents should be the celltypes annotation. mainly used the Single_data@assays$RNA@data
nfeatures	The parameter for FindVariableFeatures, NULL means select all genes
Pathway_list	(list,character) pathway gene sets list
assay	assay data of your single cell data to use,default is "RNA".
min_clustercells	Threshold for total cells fo each cluster.

Value

Pagwas list including: "Celltype_anno" "data_mat" "VariableFeatures" "merge_scexpr"

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
)

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