scorePage: scorePage

In zhilongjia/PAGE: Gene Expression Signature Similarity based on Parametric Analysis of Gene Set Enrichment

Description

Gene Expression Signature Similarity based on Parametric Analysis of Gene Set Enrichment

Usage

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)

Arguments

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 p.adjust
center	boolean
verbose	verbose

Value

a list with score, pval, fdr

References

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.

Examples

data(Psoriasis_Etanercept_LogFC)


sim <- scorePage(Psoriasis_Etanercept_LogFC, type="avg")$score

zhilongjia/PAGE documentation built on May 4, 2019, 11:22 p.m.