seurat_ref: Function to convert labelled seurat object to avg expression...

In clustifyr: Classifier for Single-cell RNA-seq Using Cell Clusters

Description

Function to convert labelled seurat object to avg expression matrix

Usage

seurat_ref(seurat_object, ...)

## S3 method for class 'seurat'
seurat_ref(
  seurat_object,
  cluster_col = "classified",
  var_genes_only = FALSE,
  assay_name = NULL,
  method = "mean",
  subclusterpower = 0,
  if_log = TRUE,
  ...
)

## S3 method for class 'Seurat'
seurat_ref(
  seurat_object,
  cluster_col = "classified",
  var_genes_only = FALSE,
  assay_name = NULL,
  method = "mean",
  subclusterpower = 0,
  if_log = TRUE,
  ...
)

Arguments

seurat_object	seurat_object after tsne or umap projections and clustering
...	additional arguments
cluster_col	column name where classified cluster names are stored in seurat meta data, cannot be "rn"
var_genes_only	whether to keep only var_genes in the final matrix output, could also look up genes used for PCA
assay_name	any additional assay data, such as ADT, to include. If more than 1, pass a vector of names
method	whether to take mean (default) or median
subclusterpower	whether to get multiple averages per original cluster
if_log	input data is natural log, averaging will be done on unlogged data

Value

reference expression matrix, with genes as row names, and cell types as column names

Examples

ref <- seurat_ref(
    seurat_object = s_small,
    cluster_col = "res.1",
    var_genes_only = TRUE
)
ref[1:3, 1:3]

Example output

            0        1        2
LTB  6.119387 3.915982 3.431685
EAF2 3.085469 2.170374 0.000000
CD19 2.792883 2.003836 0.000000

clustifyr documentation built on Nov. 8, 2020, 5:32 p.m.