Set data matrices

SPATA in general distinguishes between three types of data matrices. There are count-matrices containing the raw counts, normalized-matrices containing (log-)normalized counts, and scaled-matrices containing scaled, denoised or in any other way processed and normalized count data.

The majority of SPATA-functions leans on data carried in expression matrices. They default to the one that is set as the active expression matrix - use getActiveMatrixName() to see which one it currently is. After initiating a spata-object 'scaled' should be the default. After running runAutoencoderDenoising() 'denoised' becomes the default expression matrix.

To set one of those three matrices use these functions. To add additional matrices use addExpressionMatrix().

setCountMatrix(object, count_mtr, of_sample = NA)

setDenoisedMatrix(object, denoised_mtr, of_sample = NA)

setNormalizedMatrix(object, normalized_mtr, of_sample = NA)

setScaledMatrix(object, scaled_mtr, of_sample = NA)

Arguments

object

A valid spata-object.

count_mtr, normalized_mtr, scaled_mtr, denoised_mtr

Matrices whose column names refer to the barcodes and whose rownames refer to the gene names.

of_sample

This argument is currently inactive. It might be reactivated when spata-objects can store more than one sample.

Value

A spata object containing the set input.

Details

All set*()-functions offer a save way to set certain slots of your spata-object. They do check the input for validity but effectively overwrite everything that is occupying the slot to be set - use with caution.