standard inverse average expression — iae • smartid

standard inverse average expression

iae(expr, features = NULL, thres = 0)

Arguments

expr: a matrix, features in row and cells in column
features: vector, feature names or indexes to compute
thres: numeric, cell only counts when expr > threshold, default 0

Value

a vector of inverse average expression score for each feature

Details

$$\mathbf{IAE_i} = log(1+\frac{n}{\hat N_{i,j}+1})$$ where \(n\) is the total number of cells, \(N_{i,j}\) is the counts of feature \(i\) in cell \(j\).

Examples

data <- matrix(rpois(100, 2), 10, dimnames = list(1:10))
smartid:::iae(data)
#>         1         2         3         4         5         6         7         8 
#> 0.3254224 0.3483067 0.3746934 0.4228569 0.3053816 0.5108256 0.3610133 0.4054651 
#>         9        10 
#> 0.3254224 0.3746934