predict_celltype: predict_celltyp

In ddiez/celltype: Prediction and analysis of cell types from single cell experiments

Description

predict_celltyp

Usage

predict_celltype(
  x,
  org = "mouse",
  tissue = NULL,
  name = "immgen",
  db = NULL,
  ...
)

## S3 method for class 'Seurat'
predict_celltype(
  x,
  org = "mouse",
  tissue = NULL,
  name = "immgen",
  db = NULL,
  assay.name = "data",
  gene.col = "symbol",
  ...
)

## S3 method for class 'SingleCellExperiment'
predict_celltype(
  x,
  org = "mouse",
  tissue = NULL,
  name = "immgen",
  db = NULL,
  assay.name = "logcounts",
  gene.col = "symbol",
  ...
)

## S3 method for class 'ExpressionSet'
predict_celltype(
  x,
  org = "mouse",
  tissue = NULL,
  name = "immgen",
  db = NULL,
  ...
)

## S3 method for class 'matrix'
predict_celltype(
  x,
  org = "mouse",
  tissue = NULL,
  name = "immgen",
  db = NULL,
  ...
)

Arguments

x	object with count matrix.
org	target organism.
tissue	name of the tissue.
name	name of cell type dictionary.
db	a matrix cell type dictionary.
...	arguments passed down to methods.
assay.name	name of the assay to obtain expression matrix.
gene.col	name of the column containing gene names (default: symbol).

ddiez/celltype documentation built on May 8, 2020, 9:34 p.m.