Percentage of zeros vs. library depth

Calculate and visualize the dropout rate.

Usage

zerosVsDepth(object, ...)

# S4 method for SingleCellExperiment
zerosVsDepth(object, assay = 1L)

# S4 method for SummarizedExperiment
zerosVsDepth(object, assay = 1L)

# S4 method for matrix
zerosVsDepth(object)

# S4 method for sparseMatrix
zerosVsDepth(object)

Arguments

object

Object.

assay

vector(1). Assay name or index position.

...

Additional arguments.

Value

matrix.

Note

Updated 2022-10-24.

Author

Michael Steinbaugh, Rory Kirchner

Examples

data(SingleCellExperiment_splatter, package = "AcidTest")

## SingleCellExperiment ====
object <- SingleCellExperiment_splatter
df <- zerosVsDepth(object)
summary(df)
#> [1] "DataFrame object of length 5 with 0 metadata columns"
colnames(df)
#> [1] "dropout"           "depth"             "sampleId"         
#> [4] "sampleName"        "interestingGroups"