Get DE analysis result table(s) with statistics

This function uses edgeR and limma to get DE analysis results lists for multiple comparisons. Filter out low expressed genes and obtain DE statistics by using limma::voom and limma::treat, and also create an object proc_data to store processed data.

get_de_table(data, group_col, target_group, slot = "counts", ...)

# S4 method for DGEList,character,character
get_de_table(data, group_col, target_group, slot = "counts", ...)

# S4 method for matrix,vector,character
get_de_table(data, group_col, target_group, slot = "counts", ...)

# S4 method for Matrix,vector,character
get_de_table(data, group_col, target_group, slot = "counts", ...)

# S4 method for ExpressionSet,character,character
get_de_table(data, group_col, target_group, slot = "counts", ...)

# S4 method for SummarizedExperiment,character,character
get_de_table(data, group_col, target_group, slot = "counts", ...)

# S4 method for Seurat,character,character
get_de_table(data, group_col, target_group, slot = "counts", ...)

Arguments

data

expression object

group_col

vector or character, specify the group factor or column name of coldata for DE comparisons

target_group

pattern, specify the group of interest, e.g. NK

slot

character, specify which slot to use only for DGEList, sce or seurat object, optional, default 'counts'

...

params for function de_analysis()

Value

A list of DE result table of all comparisons.

Examples

data("im_data_6")
DE_tables <- get_de_table(im_data_6, group_col = "celltype:ch1", target_group = "NK")
#>        NK-Neutrophils NK-Monocytes NK-B.cells NK-CD4 NK-CD8
#> Down             4009         3944       3146   2694   2153
#> NotSig           1476         2678       4405   4985   6183
#> Up               4926         3789       2860   2732   2075