nullDist {signet} | R Documentation |
Generate the high-scores null distribution to compute empirical p-values for each biological pathway.
nullDist(pathways, scores, n = 1000, background)
pathways |
A list of graphNEL objects. |
scores |
A data frame in which the first column corresponds to the gene ID and the second column contains the gene scores. |
n |
Number of null high-scores to compute (default = 1000). |
background |
Optional. Background distribution computed using the
|
A vector of subnetworks scores obtained under the null hypothesis.
Must be used as input of the testSubnet
function.
# Get KEGG pathways from the package graphite: # library(graphite) # kegg <- pathways("hsapiens", "kegg") # kegg_human <- lapply(kegg, pathwayGraph) data(daub13) # load the gene scores # generate the null distribution (here, only 5 values, but # at least 1000 are advised) null <- nullDist(kegg_human, scores, n = 5)