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Check and report the type of data in Seurat object

Source: R/CheckData.R
CheckDataType.Rd

This function checks and returns a string indicating the type of data. It checks for the presence of infinite values, negative values, and whether the values are floats or integers.

Usage

CheckDataType(object, ...)

# S3 method for class 'Seurat'
CheckDataType(object, layer = "data", assay = NULL, verbose = TRUE, ...)

# Default S3 method
CheckDataType(object, verbose = TRUE, ...)

Arguments

object

A Seurat object or a matrix.

...

The message to print.

layer

Which layer to use. Default is data.

assay

Which assay to use. If NULL, the default assay of the Seurat object will be used. When the object also contains ChromatinAssay, the default assay and additional ChromatinAssay will be preprocessed sequentially.

verbose

Whether to print the message. Default is TRUE.

Value

A string indicating the type of data. Possible values are: "raw_counts", "log_normalized_counts", "raw_normalized_counts", or "unknown".

Examples

data(pancreas_sub)
CheckDataType(pancreas_sub)
#> Warning: Layer ‘data’ is empty
#> Warning: no non-missing arguments to min; returning Inf
#> Warning: no non-missing arguments to max; returning -Inf
#> Warning: no non-missing arguments to max; returning -Inf
#> ! [2026-04-26 00:57:22] Infinite values detected
#> [1] "unknown"