smooth: Smooth gene expression using the cell state graph

In juliendelile/Antler: ANother Transcriptome Lineage ExploreR

Description

This function proposes two methods to smooth the gene expression levels: a simple average over the cells' local neighborhood or a more advanced diffusion-based imputation inspired by the "Rmagic" package.

Arguments

method	a character string among: 'average' to smooth by averaging gene expression over the cell neighbors of the cell state graph (default). 'diffusion' to smooth by diffusing the gene expression levels on the cell state graph.
from	character string. Specifies whether the original gene expression levels used are raw ("Raw"), normalized ("Normalized") or have been imputed ("Smoothed"). Default to "Normalized".

juliendelile/Antler documentation built on June 19, 2021, 9 a.m.