doPareto: Prioritization of genes based on Z scores

In intePareto: Integrative Analysis of RNA-Seq and ChIP-Seq Data

Description

doPareto takes the Z scores of several different histone modifications as input, the prioritization of genes based on Z scores can be formulated as multiobjective optimization problem and solved with Pareto optimization.

Usage

doPareto(df_final, objective, nr.fronts)

Arguments

df_final	a data frame which is the output of doIntegration.
objective	a data frame which include column of "mark" column indicates the z scores of markers of histone modifications (e.g. "z.H3K4me3"), and a column named "obj" indicates the direction of the operation on the z scores, one of "max" and "min".
nr.fronts	the number of the pareto fronts you want to get.

Value

a data.frame ranked by the level of pareto fronts.

Examples

data("df_final")
objective <- data.frame(mark = c("z.H3K27ac","z.H3K4me3"),
                        obj=c("max","max"),stringsAsFactors=FALSE)
nr.fronts <- 3
doPareto(df_final = df_final,
         objective = objective,
         nr.fronts = nr.fronts)

intePareto documentation built on June 18, 2021, 5:08 p.m.