Topic 4-01: CePa

Zuguang Gu

2024-01-26

Source: vignettes/topic4_01_CePa.Rmd

CePa

The CePa package has not been updated for ~10 years. I am planning to revisit it some time this year.

It will try fix different centralities:

  • equal.weight
  • in.degree
  • out.degree
  • node betweenness
  • in.reach
  • out.reach
library(CePa)
data(PID.db)
data(gene.list)

dif and bk are two gene vectors, pc is in a special format.

# around 5min
res = cepa.ora.all(dif = gene.list$dif, bk = gene.list$bk, pc = PID.db$NCI)

Heatmap of adjusted p-values:

plot(res, adj.method = "BH", only.sig = TRUE)

We can see “e2f_pathway” is signinicant with in-degree but not significant with out-degree. Let’s directly plot the pathway network:

Plot network for a specific pathway under a specific centrality

plot(res, "e2f_pathway", cen = "in.degree")

plot(res, "e2f_pathway", cen = "out.degree")