prs {ToPASeq} | R Documentation |
This function implements the PRS method to analyze pathway enrichment of gene expression data. For PRS, a gene weight correspond to the number of downstream differentially expressed genes.
prs(de, all, pwys, nperm = 1000) prsWeights(pwy, de, all)
de |
A named numeric vector containing log2 fold-changes of the differentially expressed genes. Recommended names are Entrez gene IDs. |
all |
A character vector with the gene IDs in the reference set. If the
data was obtained from a gene expression experiment, this set will
contain all genes measured in the experiment. This vector should contain
*all* names of the |
pwys |
A |
nperm |
Integer. Number of permutations. |
pwy |
A |
A data.frame
with normalized score and p-value for each
pathway analyzed.
Ivana Ihnatova
Ibrahim et al. (2012) A topology-based score for pathway enrichment. J Comput Biol, 19(5):563-73.
# pathways library(graphite) pwys <- pathways("hsapiens","kegg")[1:10] # expression data all <- nodes(pwys[[1]]) nds <- sample(all, 30) de <- setNames(rnorm(30), nds) # executing PRS prsWeights(pwys[[1]], de, all) prs(de, all, pwys, nperm=100)