RGBM: Regularized Gradient Boosting Machine for inferring GRN

RGBMR Documentation

Regularized Gradient Boosting Machine for inferring GRN

Description

This function performs the proposed regularized gradient boosting machines for reverse engineering GRN. It allows the user to provide prior information in the form of a mechanistic network g_M and after generation of an initially inferred GRN using the core GBM model undergoes a pruning step. Here we detect and remove isolated nodes using the select_ideal_k function along with identification of the optimal set of transcription factors for each target gene. We then re-iterate through the GBM followed by the refinement step to generate the final re-constructed GRN.

Usage

RGBM(E = matrix(rnorm(100), 10, 10), K = matrix(0, nrow(E), ncol(E)), 
     g_M = matrix(1, 10, 10), tfs = paste0("G", c(1:10)), 
     targets = paste0("G", c(1:10)), lf = 1, M = 5000, nu = 0.001, s_f = 0.3,
     no_iterations = 2, mink = 0, experimentid = 1, outputpath= "DEFAULT",
     sample_type = "Exp1_", real = 0)

Arguments

E

N-by-p expression matrix. Columns correspond to genes, rows correspond to experiments. E is expected to be already normalized using standard methods, for example RMA. Colnames of E is the set of all p genes and Ntfs represents the number of transcription factors and Ntargets represents the number of target genes.

K

N-by-p initial perturbation matrix. It directly corresponds to E matrix, e.g. if K[i,j] is equal to 1, it means that gene j was knocked-out in experiment i. Single gene knock-out experiments are rows of K with only one value 1. Colnames of K is set to be the set of all genes. By default it's a matrix of zeros of the same size as E, e.g. unknown initial perturbation state of genes.

g_M

Initial mechanistic network in the form of an adajcency matrix (Ntf-by-Ntargets). Here each column is a binary vector where only those elements are 1 when the corresponding transcription factor has a connection with that target gene. Colnames of g_M should be same as names of targets and Rownames of g_M should be same as names of Tfs. By default it's a matrix of ones of size Ntfs x Ntargets.

tfs

List of names of transcription factors

targets

List of names of target genes

lf

Loss Function: 1 -> Least Squares and 2 -> Least Absolute Deviation

M

Number of extensions in boosting model, e.g. number of iterations of the main loop of RGBM algorithm. By default it's 5000.

nu

Shrinkage factor, learning rate, 0<nu<=1. Each extension to boosting model will be multiplied by the learning rate. By default it's 0.001.

s_f

Sampling rate of transcription factors, 0<s_f<=1. Fraction of transcription factors from E, as indicated by tfs vector, which will be sampled without replacement to calculate each extesion in boosting model. By default it's 0.3.

no_iterations

Number of times initial GRN to be constructed and then averaged to generate smooth edge weights for the initial GRN as shown in first_GBM_step

mink

specified threshold i.e. the minimum number of Tfs to be considered while optimizing the L-curve criterion. By default it's 0.

experimentid

The id of the experiment being conducted. It takes natural numbers like 1,2,3 etc. By default it's 1.

outputpath

Location where intermediate Adjacency_Matrix and Images folder will be created. By default it's a temp directory (e.g. /tmp/Rtmp...)

sample_type

String arguement representing a label for the experiment i.e. in case of DREAM3 challenge sample_type="DREAM3".

real

Numeric value 0 or 1 corresponding to simulated or real experiment respectively.

Value

Returns the final inferred GRN of form Ntfs-by-Ntargets adjacency matrix.

Author(s)

Raghvendra Mall <rmall@hbku.edu.qa>

See Also

select_ideal_k, first_GBM_step

Examples

# load RGBM library
library("RGBM")
# this step is optional, it helps speed up calculations, run in parallel on 2 processors
library(doParallel)
cl <- makeCluster(2)
# run network inference on a 100-by-100 dummy expression data.
A = RGBM()
stopCluster(cl)


RGBM documentation built on Aug. 11, 2022, 5:10 p.m.

Related to RGBM in RGBM...