Get the Rank of the Mean expression for each Gene in each Group

Source: R/rank_group.R

This function finds the rank of each gene's mean expression all cells in a group. This data is used to compute the rank invariance value for each gene later with rank_invariance().

rank_group(sce, group_col = "cellType", assay = "logcounts")

Arguments

sce

SummarizedExperiment-class object with the assay (defaults to logcounts).

group_col

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

assay

A character(1) specifying the name of the assay() in the sce object to use to rank expression values. Defaults to logcounts since it typically contains the normalized expression values.

Value

Named list() of ranks for each gene.

See also

Other invariance functions: rank_cells(), rank_invariance_express(), rank_invariance()

Examples

## Rank the genes for each group defined by "group" column
rank_group(sce_zero_test, group_col = "group")
#> $A_Back
#>   g100    g50     g0 gOffOn   gVar 
#>    1.0    3.5    5.0    2.0    3.5 
#> 
#> $A_Front
#>   g100    g50     g0 gOffOn   gVar 
#>      1      3      5      4      2 
#> 
#> $B_Back
#>   g100    g50     g0 gOffOn   gVar 
#>      1      3      5      2      4 
#> 
#> $B_Front
#>   g100    g50     g0 gOffOn   gVar 
#>    1.0    2.0    5.0    3.5    3.5 
#>