dat {ccRemover}

A simulated scRNA-Seq data.

Description

This data contains expression levels (log-transformed and centered) for 50 cells and 2000 genes. The 50 cells are randomly assigned to two cell types and three cell-cycle stages. 400 genes are assigned as cell-cycle genes, and the other 1600 genes are control genes. For descriptions of how we generated this data, please refer to the paper.

Usage

data(dat)

Format

A list that contains the following attributes (only x and if.cc are used by ccRemover.main.)

x

the data matrix. rows are genes, and columns are cells. These should be treated as log-transformed and centered (each row has mean 0) expression levels.

if.cc

a vector of values FALSE's or TRUE's, denoting whether the genes are cell-cycle related or control.

n

the number of cells. n=ncol(x).

p

the number of genes. p=nrow(x).

pc

the number of cell-cycle genes. pc=sum(if.cc).

ct

cell types. a vector of values 1 and 2.

cc

cell-cycle stages. a vector of values 1, 2, or 3.

Value

A simulated dataset used to demonstrate the application of ccRemover