scCount_data_input: scCount_data_input

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

scCount_data_input

Description

Input the scCount data in dataframe or matrix, the rownames is gene names, the colnames is cell names.

Usage

scCount_data_input(
  Pagwas,
  count_data,
  meta_data,
  Pathway_list,
  min_clustercells
)

Arguments

Pagwas	Pagwas format
count_data	(data.frame or matrix) count data of your single cell data to use, the rownames is gene names, the colnames is cell names.
meta_data	(data.frame) meta data of your single cell data to use, the first column is cell names. the cell names should be the same as the first row of count_data. It should include the "cell_type" column.
Pathway_list	(list,character) pathway gene sets list
min_clustercells	Threshold for total cells fo each cluster.

Value

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

Author(s)

Chunyu Deng

Examples

library(scPagwas)

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