checkCelliDArg: Check for CelliD arguments

In RausellLab/CelliD: Unbiased Extraction of Single Cell gene signatures using Multiple Correspondence Analysis

Check for CelliD arguments

Description

Performs multiple check of consistency of the argument provided by the user for different CelliD functions. It notably check if the provided features or cells name ar e actually contained in the high level object.

Usage

checkCelliDArg(X, group.by, reduction, dims, features, cells)

## S3 method for class 'Seurat'
checkCelliDArg(
  X,
  group.by = NULL,
  reduction,
  dims,
  features = NULL,
  cells = NULL
)

## S3 method for class 'SingleCellExperiment'
checkCelliDArg(
  X,
  reduction,
  dims,
  features = NULL,
  cells = NULL,
  group.by = NULL
)

Arguments

X	Seurat or SingleCell Experiment Object
group.by	Name of meta.data or ColData column.
reduction	Which dimensionality reduction to use, must be based on MCA.
dims	A vector of integers indicating which dimensions to use of specified reduction embeddings and loadings.
features	Character vector of feature names to subset feature coordinates. If not specified will take all features available from specified reduction loadings.
cells	Character vector of cell names to subset cell coordinates. If not specified will take all features available from specified reduction Embeddigns.

Value

list of corrected arguments if no error is thrown.

RausellLab/CelliD documentation built on Jan. 12, 2024, 3:44 a.m.