add_names |
Function to add names to network for the user. |
AUPR_AUROC_matrix |
Function to calculate the AUROC and AUPR of a known network. This function was made to test the R implementation of the KBoost Package. |
d4_mfac |
Function to obtain the AUPR and AUROC in the DREAM4 Multifactorial Challenge. |
D4_multi_1 |
Dream 4 multifactorial pertubation challenge dataset 1 |
D4_multi_2 |
Dream 4 multifactorial pertubation challenge dataset 2 |
D4_multi_3 |
Dream 4 multifactorial pertubation challenge dataset 3 |
D4_multi_4 |
Dream 4 multifactorial pertubation challenge dataset 4 |
D4_multi_5 |
Dream 4 multifactorial pertubation challenge dataset 5 |
Gerstein_Prior_ENET_2 |
Gene Regulatory Network from human ChIP-Seq data in Encode |
get_prior_Gerstein |
Function to build a prior using a previously built Network on ChIP-Seq. |
get_tfs_human |
Function to automatically assign Human TFs given a list of Symbols. |
grid_search_kboost |
Function to perform a grid search and find the hyperparameters. |
G_D4_multi_1 |
Gold Standard Dream 4 multifactorial pertubation challenge dataset 1 |
G_D4_multi_2 |
Gold Standard Dream 4 multifactorial pertubation challenge dataset 2 |
G_D4_multi_3 |
Gold Standard Dream 4 multifactorial pertubation challenge dataset 3 |
G_D4_multi_4 |
Gold Standard Dream 4 multifactorial pertubation challenge dataset 4 |
G_D4_multi_5 |
Gold Standard Dream 4 multifactorial pertubation challenge dataset 5 |
Human_TFs |
Index of human genes' Symbols, Entrez and Ensembl for K-Boost Pacakge that correspond to transcription factors. |
irma_check |
Function to produce the AUPR and AUROC Results on the IRMA datasets. |
IRMA_Gold |
IRMA Gold Standard Network |
irma_off |
IRMA Off Dataset |
irma_on |
IRMA On Dataset |
kboost |
A function to run KBoost. |
KBoost_human_symbol |
Function for KBoost on data from a human sample annotated with Symbol names. |
kernel_normal |
A function to perform feature normalization in kernel space. |
kernel_pc_boosting |
Function to perform Kernel Principal Component Boosting |
KPC |
Function to calculate the principal components of a kernel. |
net_dist_bin |
Function to calculate the distance between nodes. |
net_refine |
Function to do a heuristic post-processing that improves accuracy. Each column is multiplied by its variance. |
net_summary_bin |
Function to summarize the GRN filtered with a threshold, |
RBF_K |
Function to calculate the RBF Kernel of a matrix X with width g. |
tab_2_matrix_D4 |
Function to produce the gold standard of the DREAM4 Multifactorial Challenge in matrix format. |
write_GRN_D4 |
Function to write output in DREAM4 Challenge Format. |