XSumScore: XSum

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

Description

The implementation of XSum

Usage

XSumScore(refMatrix, queryUp, queryDown, topN = 500,
  permuteNum = 10000, pAdjMethod = "BH", mcCore = 1)

Arguments

refMatrix	A matrix
queryUp, queryDown	character vectors.
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

'XSumScore()' 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)))
Up <- c("gene1", "gene2")
Down <- c("gene9", "gene10")
XSumScore(refMatrix = ref, queryUp = Up, queryDown = Down, topN = 4)

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