object_ref: Function to convert labelled object to avg expression matrix

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

Description

Function to convert labelled object to avg expression matrix

Usage

object_ref(input, ...)

## Default S3 method:
object_ref(
  input,
  cluster_col = NULL,
  var_genes_only = FALSE,
  assay_name = NULL,
  method = "mean",
  lookuptable = NULL,
  if_log = TRUE,
  ...
)

## S3 method for class 'Seurat'
object_ref(
  input,
  cluster_col = NULL,
  var_genes_only = FALSE,
  assay_name = NULL,
  method = "mean",
  lookuptable = NULL,
  if_log = TRUE,
  ...
)

## S3 method for class 'seurat'
object_ref(
  input,
  cluster_col = NULL,
  var_genes_only = FALSE,
  assay_name = NULL,
  method = "mean",
  lookuptable = NULL,
  if_log = TRUE,
  ...
)

## S3 method for class 'SingleCellExperiment'
object_ref(
  input,
  cluster_col = NULL,
  var_genes_only = FALSE,
  assay_name = NULL,
  method = "mean",
  lookuptable = NULL,
  if_log = TRUE,
  ...
)

Arguments

input	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
lookuptable	if not supplied, will look in built-in table for object parsing
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

object_ref(
    s_small3,
    cluster_col = "RNA_snn_res.1"
)

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