getregcovDat: getregcovDat

In MinJinHa/PRECISE: Personalized Cancer-specific Integrated Network Estimation

Description

This function is to obtain a RPPA response vectors and covariate matrices from mRNA, miRNA, methylation data, and protein regulations from the estimated graph (G)

Usage

getregcovDat(Gmat, RPPAdat, mRNA = NULL, miRNA = NULL, Methylation = NULL, anno.miRNA = NULL, anno.methyl = NULL, integrative = T)

Arguments

Gmat	p x p adjacency matrix (row->column) which includes weights for edges
RPPAdat	n x p protein expression matrix
mRNA	a list including mRNA Data (p_mRNA x n matrix) and Des (p_mRNA x 2 matrix including GeneSymbol and EntrezID)
miRNA	a list including miRNA Data (p_miRNA x n matrix) and Des (p_mRNA x 1 matrix including miRNA names)
Methylation	a list including Methylation Data (p_methyl x n matrix) and Des (p_methyl x 4 matrix including REF, GeneSymbol, ChromosomeID and Coordinate ID). Only the cg numbers are used.
anno.miRNA	annotation matrix for miRNA including gene name in the first column and miRNA names in the second column
anno.methyl	annotation matrix for Methylation including gene name in the first column and Methylation names in the second column
integrative	TRUE if use miRNA, Methylation, and mRNA

Value

ylist	a list including scaled protein response vectors for all nodes
Xlist	a list including scaled covariate matrices for all nodes

Note

Note: all samples should be matched. The rows of RPPAdata and columns of mRNA$Data, miRNA$Data, Methylation$Data should be matched.

MinJinHa/PRECISE documentation built on May 4, 2019, 1:07 p.m.