assignPROGENyScores: 'assignPROGENyScores'

In saezlab/CARNIVAL-Bioconductor-Dev: A CAusal Reasoning tool for Network Identification (from gene expression data) using Integer VALue programming

Description

assignPROGENyScores

Usage

assignPROGENyScores(progeny = progeny, 
                                progenyMembers = progenyMembers, 
                                id = "gene", access_idx = 1)

Arguments

progeny	contains the progeny scores as obtained from runPROGENy
progenyMembers	Contains the list of members for each PROGENy pathway
id	Contains the members identifiers (default: gene)
access_idx	index of the sample to consider (default set to access_idx = 1 - assign progeny scores the first sample (if all, set access_idx = 1:nrow(progeny)))

Value

This function is used to account for the PROGENy scores in the objective function. It creates a list object with progeny scores for a selected set of samples (by default for all of them)

Author(s)

Enio Gjerga

Examples

library(CARNIVAL)
library(progeny)

expr <- as.matrix(read.csv(system.file("extdata", "human_input.csv", 
                                              package = "progeny"), 
                                              row.names = 1))

human_def_act <- progeny(expr, scale = TRUE,  organism = "Human", top = 100, 
                         perm = 10000, z_scores = FALSE)


## loading the progeny members to assign the weights
load(file = system.file("progenyMembers.RData",package="CARNIVAL"))
# load(file = "progenyMembers.RData")

## now assigning the PROGENy weights to pathway members only for the first 
## sample which we can consider for the CARNIVAL analysis
weightObj <- assignPROGENyScores(progeny = human_def_act, 
                                 progenyMembers = progenyMembers, 
                                 id = "gene", access_idx = 1)

saezlab/CARNIVAL-Bioconductor-Dev documentation built on Aug. 30, 2020, 2:39 p.m.