ZhangScore: ZhangScore

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

Description

The implementation of ZhangScore

Usage

ZhangScore(refMatrix, queryUp, queryDown, permuteNum = 10000,
  pAdjMethod = "BH", mcCore = 1)

Arguments

refMatrix	A matrix
queryUp, queryDown	character vectors. if there is no up or down signatures, you should set: queryUp = NULL or queryDown = NULL.
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

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

References

"Zhang S D et al. BMC bioinformatics, 2008, 9(1): 258".

Examples

set.seed(1234)
ref <- matrix(rnorm(1000), nrow = 10,
  dimnames = list(paste0("gene", 1:10), paste0("drug", 1:100)))
Up <- c("gene1", "gene2")
Down <- c("gene9", "gene10")
ZhangScore(refMatrix = ref, queryUp = Up, queryDown = Down)

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