fetch_HVGs: Fetch the variable genes of cell subsets by different...

In YinanZhang522/SIEVE: identify SIngle-cEll Variable gEnes for single-cell RNA sequencing data

Description

Fetch the variable genes of cell subsets by different methods.

Usage

fetch_HVGs(dataframe,celllist,method=method,n=50)

Arguments

dataframe	A gene expression dataframe, can be raw counts or normalized data, rows should be genes, columns should be cells.
celllist	A matrix returned from fetch_cells
method	the method used to fetch the variable genes,if your data is a raw counts matrix, method should be chosen from "M3Drop","ROGUE","Scran","Scmap".if your data is a normalized matrix, method should be chosen from "schs"(singleCellHaystack),"Seurat_vst","Seurat_disp","Seurat_sct","ROGUE".
n	The number of feature genes.The default value of n is set to 2000.

Value

A list of HVGs.

Examples

genelist<-fetch_HVGs(dataframe,celllist,method=method,n=2000)

YinanZhang522/SIEVE documentation built on March 27, 2021, 9:12 a.m.