XCosScore: XCos

In Jasonlinchina/RCSM: RCSM(Recommended Connectivity-map Scoring Methods)

Description

The implementation of XCos

Usage

XCosScore(refMatrix, query, topN = 500, permuteNum = 10000,
  pAdjMethod = "BH", mcCore = 1)

Arguments

refMatrix	A matrix
query	A numeric vector with names.
topN	number of genes in top and bottom of reference gene list
permuteNum	number of perturbation time for computing pValue
pAdjMethod	method to use for computing adjudted-pValue
mcCore	the number of core to use for parallel computing

Details

'XCosScore()' returns a data.frame, each row of which contains score, pValue and adjusted-pValue for one sample in the refMatrix.

References

"Cheng J et al. Genome medicine, 2014, 6(12): 95".

Examples

set.seed(1234)
ref <- matrix(rnorm(1000), nrow = 10,
  dimnames = list(paste0("gene", 1:10), paste0("drug", 1:100)))
query <- rnorm(4)
names(query) <- c("gene1", "gene2", "gene9", "gene10")
XCosScore(refMatrix = ref, query = query, topN = 4)

Jasonlinchina/RCSM documentation built on Aug. 4, 2019, 12:46 p.m.