P_null {pageRank} | R Documentation |
Build null model for evaluating the significance of interactions by generating random regulator-target pairs.
P_null(expmat, net, n = 10000, sep = 5, method = c("difference", "mi"))
expmat |
(matrix) Gene expression matrix. |
net |
(data.frame) Network, with "reg" and "target" in column name. |
n |
(numeric) Number of random pairs. |
sep |
(numeric) Number of bins for calculating marginal/joint probability. |
method |
(character) Method for calculating probability-based distance, either PXY-PXPY ("difference") or mutual information ("mi"). |
(ecdf) ECDF of null distribution.
DING, HONGXU (hd2326@columbia.edu)
library(bcellViper) data(bcellViper) dset <- exprs(dset) net <- do.call(rbind, lapply(1:10, function(i, regulon){ data.frame(reg=rep(names(regulon)[i], 10), target=names(regulon[[i]][[1]])[1:10], direction=rep(1, 10), stringsAsFactors = FALSE)}, regulon=regulon)) P_null(dset, net, n=100, method="difference")