## ---- echo=FALSE--------------------------------------------------------- library(GenRank) input_file <- system.file("extdata","CE_toydata.txt",package="GenRank") toydata <- read.table(input_file,header=FALSE, sep = '\t') head(toydata) ## ---- echo=FALSE--------------------------------------------------------- library(GenRank) input_file <- system.file("extdata","CE_toydata.txt",package="GenRank") toydata <- read.table(input_file,header=FALSE, sep = '\t') head(toydata[,1:2]) ## ------------------------------------------------------------------------ library(GenRank) input_file <- system.file("extdata","CE_toydata.txt",package="GenRank") CE_ranks <- ComputeCE(input_file,PC = "equal") head(CE_ranks) ## ------------------------------------------------------------------------ evid.weight <- c(1,1,0.8,0.8,0.5,1) ## ------------------------------------------------------------------------ file1 <- read.table(input_file, header = FALSE, sep = "\t", stringsAsFactors = FALSE) names(table(file1[,2])) ## ------------------------------------------------------------------------ CE_ranks_cust <- ComputeCE(input_file,PC = "custom", cust.weights = evid.weight) head(CE_ranks_cust) ## ------------------------------------------------------------------------ library(GenRank) input_file <- system.file("extdata","RP_toydata.txt",package="GenRank") signif.val <- c('L','L','H','L','H','L') RP_ranks <- ComputeRP(input_file, signif.type = signif.val) head(RP_ranks) ## ------------------------------------------------------------------------ RP_ranks_cust <- ComputeRP(input_file, signif.type = signif.val, n.perm=200, setseed=1234) head(RP_ranks_cust) ## ------------------------------------------------------------------------ library(GenRank) input_file_P <- system.file("extdata","CombP_toydata.txt",package="GenRank") CP_ranking <- CombP(input_file_P, method = "fisher", na.remove = TRUE) head(CP_ranking) ## ------------------------------------------------------------------------ cus.weights <- c(100,50,200,300,150,400) CP_ranking_z <- CombP(input_file_P, method = "z.transform", na.remove = TRUE, weight = cus.weights) head(CP_ranking_z)