PrepareData: Prepare the data

Description Usage Arguments Value

View source: R/LRC3_Alpha.R

Description

This function is to prepare the data.

Usage

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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.