scCount_data_input — scCount_data

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
)

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.

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

Chunyu Deng

library(scPagwas)