AddSmoothedScore: Calculate smoothed expression values

In nukappa/seurat_v2: Seurat : R toolkit for single cell genomics

Description

Smooths expression values across the k-nearest neighbors based on dimensional reduction

Usage

AddSmoothedScore(object, genes.fit = NULL, dim.1 = 1, dim.2 = 2,
  reduction.use = "tsne", k = 30, do.log = FALSE, do.print = FALSE)

Arguments

object	Seurat object
genes.fit	Genes to calculate smoothed values for
dim.1	Dimension for x-axis (default 1)
dim.2	Dimension for y-axis (default 2)
reduction.use	Which dimensionality reduction to use. Default is "tsne", can also be "pca", or "ica", assuming these are precomputed.
k	k-param for k-nearest neighbor calculation
do.log	Whether to perform smoothing in log space. Default is false.
do.print	Print progress (output the name of each gene after it has been imputed).

nukappa/seurat_v2 documentation built on May 24, 2019, 9:57 a.m.