Run.GroupTechEffects {GTEs} | R Documentation |
Compute the group technical effects.
Description
Compute the group technical effects.
Usage
Run.GroupTechEffects(X, meta, g_factor, b_factor, do.scale = FALSE)
Arguments
X |
Input data matrix. |
meta |
Input metadata (data.frame). |
g_factor |
Group variable (s). |
b_factor |
Batch variable (s). |
do.scale |
Whether to perform scaling. |
Value
A list containing the overall GTE ($OverallTechEffects) and the GTE ($GroupTechEffects) of each subgroup under the group variable.
Examples
# X is a normalized expression matrix with rows as features and columns as cells.
# meta is a data.frame with columns containing metadata such as cell type, batch, etc.
data_file <- system.file("extdata", "example_data.rds", package = "GTEs")
example_data <- readRDS(data_file)
meta_file <- system.file("extdata", "example_meta.rds", package = "GTEs")
example_meta <- readRDS(meta_file)
GTE_ct <- Run.GroupTechEffects(example_data, example_meta,
g_factor = "CellType",
b_factor = "Batch")
[Package GTEs version 1.0.0 Index]