Get the Proportion of Zero Counts for Each Gene in Each Group

This function calculates the Proportion Zero for each gene in each user defined group. Proportion Zero = number of zero counts for a gene for a group of cells/number of cells in the group.

get_prop_zero(sce, group_col = "cellType")

Arguments

sce

SummarizedExperiment-class object

group_col

name of the column in the colData() of sce that defines the group of interest.

Value

A data.frame() containing proportion of zero counts, genes as rows, groups as columns.

Details

For more information about calculating Proportion Zero, check equation 1 from the vignette in section "Calculate Proportion Zero and Pick Cutoff".

See also

Other Proportion Zero functions: filter_prop_zero()

Examples

## Basic Proportion counts == 0
rowSums(assays(sce_zero_test)$counts == 0) / ncol(sce_zero_test)
#>   g100    g50     g0 gOffOn   gVar 
#>   1.00   0.50   0.00   0.50   0.47 

## Get proportion by the default group "cellType"
get_prop_zero(sce_zero_test)
#>           A    B
#> g100   1.00 1.00
#> g50    0.48 0.52
#> g0     0.00 0.00
#> gOffOn 0.50 0.50
#> gVar   0.58 0.36

## Get proportion by user defined grouping of the data
get_prop_zero(sce_zero_test, group_col = "group")
#>        A_Back A_Front B_Back B_Front
#> g100     1.00    1.00   1.00    1.00
#> g50      0.48    0.48   0.52    0.52
#> g0       0.00    0.00   0.00    0.00
#> gOffOn   0.60    0.40   0.60    0.40
#> gVar     0.48    0.68   0.32    0.40

## Groups with missing levels will be dropped
get_prop_zero(sce_zero_test, group_col = "cellType_na")
#> Warning: Dropping Empty Levels in group_col: cellType_na
#>           A    B
#> g100   1.00 1.00
#> g50    0.48 0.52
#> g0     0.00 0.00
#> gOffOn 0.50 0.50
#> gVar   0.58 0.36