rawParse: Parsing the data to get top expressed genes

In Coolgenome/iTALK: Characterize and Illustrate Intercellular Communication

Description

This function loads the count data as a dataframe. It assumes that each line contains gene expression profile of one single cell, and each column contains the one single gene expression profile in different cells. The dataframe should also contain the cell type information with column name 'cell_type'. Group information should also be included as 'compare_group' if users want to call differntial expressed ligand-receptor pairs. Batch information as 'batch' is optional. If included, users may want to use the raw count data for later analysis.

Usage

rawParse(data, top_genes = 50, stats = "mean")

Arguments

data	Input data, raw or normalized count with 'cell_type' column
top_genes	(scale 1 to 100) Top percent highly expressed genes used to find ligand-receptor pairs, default is 50
stats	Whether calculates the mean or the median of the data. Available options are 'mean' and 'median'.

Value

A dataframe of the data

Coolgenome/iTALK documentation built on Aug. 3, 2019, 3:12 p.m.