Seurat (version 2.0.0)

AddSmoothedScore: Calculate smoothed expression values

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).