Description Usage Arguments Value References Examples
Gene Expression Signature Similarity based on Parametric Analysis of Gene Set Enrichment
1 2 3 4 5 6 7 8 9 10 11 12 | scorePage(dat, top = 250, ncore = 2, type = c("avg", "max"),
similarity = TRUE, adjust = "fdr", center = TRUE, verbose = FALSE)
## S4 method for signature 'matrix'
scorePage(dat, top = 250, ncore = 2, type = c("avg",
"max"), similarity = TRUE, adjust = "fdr", center = TRUE,
verbose = FALSE)
## S4 method for signature 'list'
scorePage(dat, top = 250, ncore = 2, type = c("avg",
"max"), similarity = TRUE, adjust = "fdr", center = TRUE,
verbose = FALSE)
|
dat |
logFC matrix or list |
top |
top genes selected |
ncore |
the number of cores used |
type |
avg or max |
similarity |
boolean |
adjust |
p.adjust.methods. see |
center |
boolean |
verbose |
verbose |
a list with score, pval, fdr
1. Kim, Seon-Young, and David J. Volsky. "PAGE: parametric analysis of gene set enrichment." BMC bioinformatics 6.1 (2005): 1.
2. Iorio, Francesco, et al. "Discovery of drug mode of action and drug repositioning from transcriptional responses." Proceedings of the National Academy of Sciences 107.33 (2010): 14621-14626.
1 2 3 4 | data(Psoriasis_Etanercept_LogFC)
sim <- scorePage(Psoriasis_Etanercept_LogFC, type="avg")$score
|
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