select_gene: Select variable gene from single-cell RNA-seq data

In WeiqiangZhou/SINTER: Single-cell genomic data integration

Description

This function is used for selecting variable gene from scRNA-seq data.

Usage

select_gene(expr, RNA_train_all, filter_th = 0.1, var_th = 0.2,
  dataplot = FALSE)

Arguments

expr	Gene expression matrix of scRNA-seq (normalized counts).
RNA_train_all	Gene expression matrix of bulk RNA-seq from ENCODE.
filter_th	Threshold for filtering out genes with no expression in the given percentage of cells.
var_th	Threshold for filtering out genes with low variability in the given percentage of genes.
dataplot	Plot the mean and variance of all genes and the selected genes are highlighted.

Value

expr_select	Log2-transformed gene expression matrix of scRNA-seq for the selected genes.
RNA_train_select	Gene expression matrix of bulk RNA-seq for the selected genes.

Examples

## Not run: 
expr_data_select <- select_gene(expr_in,RNA_train_all,filter_th=0.1,var_th=0.2,dataplot=TRUE)

## End(Not run)

WeiqiangZhou/SINTER documentation built on Sept. 11, 2019, 8:03 a.m.