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

Description Usage Arguments Value Examples

View source: R/callback-functions.R

Description

A base callback function that returns a galgo.Obj

Usage

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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

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# 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.