Inference of gene regulatory networks from gene expression data

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Documentation for package ‘KBoost’ version 1.1.0

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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.