ComputeCE: Convergent Evidence (CE) scores of genes.

In GenRank: Candidate gene prioritization based on convergent evidence

Description

ComputeCE returns ranks of the genes based on CE scores.

Usage

ComputeCE(file, PC = c("equal", "ngene", "custom"), cust.weights = NULL)

Arguments

file	A tab-delimited text file with a minimum of 2 columns. First column should contain gene names and second column should indicate the evidence type.
PC	A character string among 'equal', 'ngene' or 'custom' indicating the prior credibility.
cust.weights	An optional argument required when the PC='custom'. A numeric vector containing weights reflecting prior credibility. Should contain as many weights as the number of evidence types.

Value

If all the inputs are in the correct format as suggested, then the output will be a dataframe containing genes and their ranks based on CE scores.

Examples

input_file <- system.file("extdata","CE_toydata.txt",package="GenRank")
CE_ranks <- ComputeCE(input_file,PC = "equal")
evid.weight <- c(1,1,0.8,0.8,0.5,1)
CE_ranks_cust <- ComputeCE(input_file,PC = "custom", cust.weights = evid.weight)

GenRank documentation built on April 28, 2020, 7:09 p.m.