Perform differential activity analysis on expression set

Usage

getDA(
  input_eset,
  group_by = "clusterID",
  g1 = NULL,
  g0 = NULL,
  use_method = "t.test"
)

Arguments

input_eset: The expression set object that filtered, normalized and log-transformed
group_by: Character, name of the column for grouping, usually the column of cell types or clusters. Default: "clusterID".
g1: A vector of character defining the fore-ground group or NULL. Default: NULL.
g0: A vector of character defining the back-ground group or NULL. Default: NULL.
use_method: Character, method used for differential analysis: "limma", "wilcoxon", and "t.test" (the default).

Value

A data frame. Rows are genes/drivers, and columns are 11 statistics of differential analysis.

Examples

if (FALSE) { # \dontrun{
## 1. To perform differential activity analysis in a 1-vs-rest manner for all groups in "clusterID" column
da_res <- getDA(input_eset = activity_clustered.eset,
                group_by = "clusterID",
                use_method = "t.test")

## 2. To perform differential activity analysis in a 1-vs-rest manner for one specific group in "clusterID" column
da_res <- getDA(input_eset = activity_clustered.eset,
                group_by = "clusterID",
                g1 = c("1"),
                use_method = "t.test")

## 3. To perform differential activity analysis in a rest-vs-1 manner for one specific group in "clusterID" column
da_res <- getDA(input_eset = activity_clustered.eset,
                group_by = "clusterID",
                g0 = c("1"),
                use_method = "t.test")

## 4. To perform differential activity analysis in a 1-vs-1 manner for groups in "clusterID" column
da_res <- getDA(input_eset = activity_clustered.eset,
                group_by = "clusterID",
                g1 = c("1"),
                g0 = c("3"),
                use_method = "t.test")
} # }