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Calculate driver activities in batch from the SJARACNe directory

getActivity_inBatch.Rd

This function is used to calculate the driver activities of multiple groups from a scMINER directory. To calculate driver activities of one single group, please use getActivity_individual().

Usage

getActivity_inBatch(
  input_eset,
  sjaracne_dir,
  group_name,
  group_exclude = NULL,
  network_tag.tf = NULL,
  network_tag.sig = NULL,
  driver_type = "TF_SIG",
  activity_method = "mean",
  do.z_normalization = TRUE
)

Arguments

input_eset

The expression set object which has been filtered, normalized and log-transformed

sjaracne_dir

The path to the SJARACNe directory

group_name

Character, name of the column for grouping, usually the column of cell types or clusters

group_exclude

A vector of group names to exclude in activity calculation

network_tag.tf

Character or NULL, the tag used to distinguish different SJARACNe runs from the same input files. This is usually the name of the folder(s) in "TF" folder of each group. Default: NULL.

network_tag.sig

Character or NULL, the tag used to distinguish different SJARACNe runs from the same input files. This is usually the name of the folder(s) in "SIG" folder of each group. Default: NULL.

driver_type

Character, type of the pre-defined driver list to use. Should be one of: "TF" for transcriptional factors only, "SIG" for signaling genes only, or "TF_SIG" for both. Default: "TF_SIG".

activity_method

Character, method used to calculate the activity: "mean" (the default), "weightedmean", "absmean" or "maxmean".

do.z_normalization

Logical, whether to do the z-normalization on the gene expression values in each sample. Set if to FALSE only when the expression values has been scaled in each cell. Default: TRUE.

Value

A expression set object. The assayData is the activity matrix of all cells of all groups, drivers by cells. The phenoData and featureData are exactly save with the input eset.

Examples

data(pbmc14k_expression.eset)

## 1. when no tag was used in running SJARACNE: the network file folder ("sjaracne_workflow-*") is directly under TF/SIG folder of each group.
activity.eset <- getActivity_inBatch(input_eset = pbmc14k_expression.eset,
                                     sjaracne_dir = system.file("extdata/demo_pbmc14k/SJARACNe", package = "scMINER"),
                                     group_name = "trueLabel",
                                     driver_type = "TF_SIG",
                                     activity_method = "mean",
                                     do.z_normalization = TRUE)
#> 7 groups were found in trueLabel ...
#> Checking network files for each group ...
#> 	Group 1 / 7 : B ...
#> 		TF network check passed!
#> 		SIG network check passed!
#> 	Group 2 / 7 : CD4TCM ...
#> 		TF network check passed!
#> 		SIG network check passed!
#> 	Group 3 / 7 : CD4TN ...
#> 		TF network check passed!
#> 		SIG network check passed!
#> 	Group 4 / 7 : CD4Treg ...
#> 		TF network check passed!
#> 		SIG network check passed!
#> 	Group 5 / 7 : CD8TN ...
#> 		TF network check passed!
#> 		SIG network check passed!
#> 	Group 6 / 7 : Monocyte ...
#> 		TF network check passed!
#> 		SIG network check passed!
#> 	Group 7 / 7 : NK ...
#> 		TF network check passed!
#> 		SIG network check passed!
#> Calculating activity for each group ...
#> 	Group 1 / 7 : B ...
#> 	Activity calculation is completed successfully!
#> 	Group 2 / 7 : CD4TCM ...
#> 	Activity calculation is completed successfully!
#> 	Group 3 / 7 : CD4TN ...
#> 	Activity calculation is completed successfully!
#> 	Group 4 / 7 : CD4Treg ...
#> 	Activity calculation is completed successfully!
#> 	Group 5 / 7 : CD8TN ...
#> 	Activity calculation is completed successfully!
#> 	Group 6 / 7 : Monocyte ...
#> 	Activity calculation is completed successfully!
#> 	Group 7 / 7 : NK ...
#> 	Activity calculation is completed successfully!
#> NAs were found in the activity matrix and have been replaced by the minimum value:  -0.3879122 .

## 2. when tag (e.g. "bt100_pc001" ) was used: the network file folder ("sjaracne_workflow-*") is directly under a subfolder "bs_100" of the TF/SIG folder of each group.
activity.eset <- getActivity_inBatch(input_eset = pbmc14k_expression.eset,
                                     sjaracne_dir = system.file("extdata/demo_pbmc14k/SJARACNe", package = "scMINER"),
                                     group_name = "trueLabel",
                                     network_tag.tf = "bt100_pc001",
                                     network_tag.sig = "bt100_pc001",
                                     driver_type = "TF_SIG",
                                     activity_method = "mean",
                                     do.z_normalization = TRUE)
#> 7 groups were found in trueLabel ...
#> Checking network files for each group ...
#> 	Group 1 / 7 : B ...
#> 		TF network check passed!
#> 		SIG network check passed!
#> 	Group 2 / 7 : CD4TCM ...
#> 		TF network check passed!
#> 		SIG network check passed!
#> 	Group 3 / 7 : CD4TN ...
#> 		TF network check passed!
#> 		SIG network check passed!
#> 	Group 4 / 7 : CD4Treg ...
#> 		TF network check passed!
#> 		SIG network check passed!
#> 	Group 5 / 7 : CD8TN ...
#> 		TF network check passed!
#> 		SIG network check passed!
#> 	Group 6 / 7 : Monocyte ...
#> 		TF network check passed!
#> 		SIG network check passed!
#> 	Group 7 / 7 : NK ...
#> 		TF network check passed!
#> 		SIG network check passed!
#> Calculating activity for each group ...
#> 	Group 1 / 7 : B ...
#> 	Activity calculation is completed successfully!
#> 	Group 2 / 7 : CD4TCM ...
#> 	Activity calculation is completed successfully!
#> 	Group 3 / 7 : CD4TN ...
#> 	Activity calculation is completed successfully!
#> 	Group 4 / 7 : CD4Treg ...
#> 	Activity calculation is completed successfully!
#> 	Group 5 / 7 : CD8TN ...
#> 	Activity calculation is completed successfully!
#> 	Group 6 / 7 : Monocyte ...
#> 	Activity calculation is completed successfully!
#> 	Group 7 / 7 : NK ...
#> 	Activity calculation is completed successfully!
#> NAs were found in the activity matrix and have been replaced by the minimum value:  -0.3879122 .

## 3. to calculate the activities of TF only
activity.eset <- getActivity_inBatch(input_eset = pbmc14k_expression.eset,
                                     sjaracne_dir = system.file("extdata/demo_pbmc14k/SJARACNe", package = "scMINER"),
                                     group_name = "trueLabel",
                                     network_tag.tf = "bt100_pc001",
                                     network_tag.sig = "bt100_pc001",
                                     driver_type = "TF",
                                     activity_method = "mean",
                                     do.z_normalization = TRUE)
#> 7 groups were found in trueLabel ...
#> Checking network files for each group ...
#> 	Group 1 / 7 : B ...
#> 		TF network check passed!
#> 	Group 2 / 7 : CD4TCM ...
#> 		TF network check passed!
#> 	Group 3 / 7 : CD4TN ...
#> 		TF network check passed!
#> 	Group 4 / 7 : CD4Treg ...
#> 		TF network check passed!
#> 	Group 5 / 7 : CD8TN ...
#> 		TF network check passed!
#> 	Group 6 / 7 : Monocyte ...
#> 		TF network check passed!
#> 	Group 7 / 7 : NK ...
#> 		TF network check passed!
#> Calculating activity for each group ...
#> 	Group 1 / 7 : B ...
#> 	Activity calculation is completed successfully!
#> 	Group 2 / 7 : CD4TCM ...
#> 	Activity calculation is completed successfully!
#> 	Group 3 / 7 : CD4TN ...
#> 	Activity calculation is completed successfully!
#> 	Group 4 / 7 : CD4Treg ...
#> 	Activity calculation is completed successfully!
#> 	Group 5 / 7 : CD8TN ...
#> 	Activity calculation is completed successfully!
#> 	Group 6 / 7 : Monocyte ...
#> 	Activity calculation is completed successfully!
#> 	Group 7 / 7 : NK ...
#> 	Activity calculation is completed successfully!
#> NAs were found in the activity matrix and have been replaced by the minimum value:  -0.3425395 .

## 4. to exclude some groups in the activity calculation (e.g. "NK" and "Monocyte")
activity.eset <- getActivity_inBatch(input_eset = pbmc14k_expression.eset,
                                     sjaracne_dir = system.file("extdata/demo_pbmc14k/SJARACNe", package = "scMINER"),
                                     group_name = "trueLabel",
                                     group_exclude = c("NK", "Monocyte"),
                                     network_tag.tf = "bt100_pc001",
                                     network_tag.sig = "bt100_pc001",
                                     driver_type = "TF",
                                     activity_method = "mean",
                                     do.z_normalization = TRUE)
#> 7 groups were found in trueLabel ...
#> 5 groups left after excluding the groups specified by group_exclude: B, CD4TCM, CD4TN, CD4Treg, CD8TN ...
#> Checking network files for each group ...
#> 	Group 1 / 5 : B ...
#> 		TF network check passed!
#> 	Group 2 / 5 : CD4TCM ...
#> 		TF network check passed!
#> 	Group 3 / 5 : CD4TN ...
#> 		TF network check passed!
#> 	Group 4 / 5 : CD4Treg ...
#> 		TF network check passed!
#> 	Group 5 / 5 : CD8TN ...
#> 		TF network check passed!
#> Calculating activity for each group ...
#> 	Group 1 / 5 : B ...
#> 	Activity calculation is completed successfully!
#> 	Group 2 / 5 : CD4TCM ...
#> 	Activity calculation is completed successfully!
#> 	Group 3 / 5 : CD4TN ...
#> 	Activity calculation is completed successfully!
#> 	Group 4 / 5 : CD4Treg ...
#> 	Activity calculation is completed successfully!
#> 	Group 5 / 5 : CD8TN ...
#> 	Activity calculation is completed successfully!
#> NAs were found in the activity matrix and have been replaced by the minimum value:  -0.3425395 .

## 5. when calculate the activities from the gene expression values scaled by other methods (e.g. ScaleData() from Seurat package)
activity.eset <- getActivity_inBatch(input_eset = pbmc14k_expression.eset,
                                     sjaracne_dir = system.file("extdata/demo_pbmc14k/SJARACNe", package = "scMINER"),
                                     group_name = "trueLabel",
                                     network_tag.tf = "bt100_pc001",
                                     network_tag.sig = "bt100_pc001",
                                     driver_type = "TF_SIG",
                                     activity_method = "mean",
                                     do.z_normalization = FALSE)
#> 7 groups were found in trueLabel ...
#> Checking network files for each group ...
#> 	Group 1 / 7 : B ...
#> 		TF network check passed!
#> 		SIG network check passed!
#> 	Group 2 / 7 : CD4TCM ...
#> 		TF network check passed!
#> 		SIG network check passed!
#> 	Group 3 / 7 : CD4TN ...
#> 		TF network check passed!
#> 		SIG network check passed!
#> 	Group 4 / 7 : CD4Treg ...
#> 		TF network check passed!
#> 		SIG network check passed!
#> 	Group 5 / 7 : CD8TN ...
#> 		TF network check passed!
#> 		SIG network check passed!
#> 	Group 6 / 7 : Monocyte ...
#> 		TF network check passed!
#> 		SIG network check passed!
#> 	Group 7 / 7 : NK ...
#> 		TF network check passed!
#> 		SIG network check passed!
#> Calculating activity for each group ...
#> 	Group 1 / 7 : B ...
#> 	Activity calculation is completed successfully!
#> 	Group 2 / 7 : CD4TCM ...
#> 	Activity calculation is completed successfully!
#> 	Group 3 / 7 : CD4TN ...
#> 	Activity calculation is completed successfully!
#> 	Group 4 / 7 : CD4Treg ...
#> 	Activity calculation is completed successfully!
#> 	Group 5 / 7 : CD8TN ...
#> 	Activity calculation is completed successfully!
#> 	Group 6 / 7 : Monocyte ...
#> 	Activity calculation is completed successfully!
#> 	Group 7 / 7 : NK ...
#> 	Activity calculation is completed successfully!
#> NAs were found in the activity matrix and have been replaced by the minimum value:  0 .