Description Usage Arguments Value Note
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)
1 | getregcovDat(Gmat, RPPAdat, mRNA = NULL, miRNA = NULL, Methylation = NULL, anno.miRNA = NULL, anno.methyl = NULL, integrative = T)
|
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 |
ylist |
a list including scaled protein response vectors for all nodes |
Xlist |
a list including scaled covariate matrices for all nodes |
Note: all samples should be matched. The rows of RPPAdata and columns of mRNA$Data, miRNA$Data, Methylation$Data should be matched.
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