Seurat (version 2.3.4)

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,
  nn.eps = 0)

Arguments

object

Seurat object

genes.fit

Genes to calculate smoothed values for

dim.1

Dimension 1 to use for dimensional reduction

dim.2

Dimension 2 to use for dimensional reduction

reduction.use

Dimensional reduction to use

k

k-param for k-nearest neighbor calculation. 30 by default

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).

nn.eps

Error bound when performing nearest neighbor seach using RANN; default of 0.0 implies exact nearest neighbor search

Examples

# NOT RUN {
pbmc_small <- AddSmoothedScore(object = pbmc_small, genes.fit = "MS4A1", reduction.use = "pca")

# }