callback_base_return_pop: A base callback function that returns a galgo.Obj

In harpomaxx/galgoR-package: An Evolutionary Framework for the Identification and Study of Prognostic Gene Expression Signatures in Cancer

Description

A base callback function that returns a galgo.Obj

Usage

callback_base_return_pop (userdir = "",generation, pop_pool, 
pareto, prob_matrix, current_time)

Arguments

userdir	the default directory used by 'galgo()' to store files
generation	a number indicating the number of iterations of the galgo algorithm
pop_pool	a data.frame with the solution vectors, number of clusters and their ranking.
pareto	the solutions found by Galgo across all generations in the solution space
prob_matrix	a matrix or data.frame. Must be an expression matrix with features in rows and samples in columns
current_time	an POSIXct object

Value

an object of class galgo

Examples

# load example dataset

library(breastCancerTRANSBIG)
data(transbig)
Train <- transbig
rm(transbig)
expression <- Biobase::exprs(Train)
clinical <- Biobase::pData(Train)
OS <- survival::Surv(time = clinical$t.rfs, event = clinical$e.rfs)
# We will use a reduced dataset for the example
expression <- expression[sample(1:nrow(expression), 100), ]

# Now we scale the expression matrix
expression <- t(scale(t(expression)))

# Run galgo with base_return_pop_callback assigned to the end_galgo_callback
# hook-point
# By using this callback galgo() return a `galgo,Obj` object.
output <- GSgalgoR::galgo(generations = 5,
population = 15,
prob_matrix = expression,
OS = OS,
end_galgo_callback = callback_base_return_pop
)

harpomaxx/galgoR-package documentation built on Oct. 26, 2020, 7:05 a.m.