PrepareData: Prepare the data

In XiaojuanShen/LRC3: Ligand-Receptor based Communication

Description

This function is to prepare the data.

Usage

PrepareData(dd = dd, SingleCellExperimentObject = FALSE,
  log_counts = FALSE, SparseMatrix = FALSE, Species = c("Human", "Mouse"))

Arguments

dd	The input expresstion matrix. The format of the data should be a dataframe or a matrix, with rownames as the gene names, and colomn names as the cell type names. It could also be an SingleCellExperiment objects with thecell types names stored in the <e2><80><9c>cell_type1<e2><80><9d> slot of the colData.
SingleCellExperimentObject	if SingleCellExperimentObject = TRUE,the imput data format is SingleCellExperiment object, if SingleCellExperimentObject = FALSE,the imput data format is an expression matrix.
log_counts	parameter for 'SingleCellExperimentObject', if log_counts = FALSE, use none log normalized data, if log_counts = TRUE,use log normalized data.
SparseMatrix	if SparseMatrix = TRUE, the SingleCellExperimentObject input data is a sparse matrix.
Species	choosing a species of the dataset

Value

data_list an object that contain the expression matrix dd, the cell type name index, and cell type names.

XiaojuanShen/LRC3 documentation built on May 25, 2019, 6:26 p.m.