checkCelliDArg {CelliD} | R Documentation

## 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.

[Package CelliD version 1.2.1 Index]