callback_no_report: Print minimal information to the user about galgo execution.

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

Description

The main idea behind this callback function is to provide some feedback to the user about galgo execution. No other relevant information is shown

Usage

callback_no_report (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

Nothing.

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 no_report_callback assigned to the report_callback
# hook-point
GSgalgoR::galgo(generations = 5,
population = 15,
prob_matrix = expression,
OS = OS,
report_callback = callback_no_report
)

harpomaxx/GSgalgoR documentation built on Oct. 25, 2020, 3:47 p.m.