RCSM

RCSM(Recommended Connectivity-map Scoring Methods)

Description

Connecting disease gene expression signatures to compound-induced gene expression profiles is valuable for understanding drug Mechanism of Action (MoA) and applying an existing therapeutic to a new disease indication. RCSM is an R package for measuring those connectivities. RCSM implemented seven methods that are reported in published papers.

Details of seven methods

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

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

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

GSEAweight0Score(refMatrix, queryUp, queryDown, permuteNum = 10000, pAdjMethod = "BH", mcCore = 1)

GSEAweight1Score(refMatrix, queryUp, queryDown, permuteNum = 10000, pAdjMethod = "BH", mcCore = 1)

GSEAweight2Score(refMatrix, queryUp, queryDown, permuteNum = 10000, pAdjMethod = "BH", mcCore = 1)

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

How to install this package?

install.packages("devtools")

library(devtools)

install_github("Jasonlinchina/RCSM")

library(RCSM)

If there is any bug or suggestion, please contact kequanlin@gmail.com

FAQ

1, If you encounter the error saying "readRDS(dest) XXX" when installing the RCSM, you could first remove the old version of RCSM with "remove.packages("RCSM")", and then restart the R or Rstudio.