find_max_sum_submatrix

Main function to find the maximum sum deltaZ score submatrix using GA to optimize the screening layout of seed and partner drivers.

Usage

find_max_sum_submatrix(
  matrix,
  n,
  m,
  use_popSize = 50,
  use_maxiter = 100,
  use_run = 50,
  use_suggestions = NULL
)

Arguments

matrix

a deltaZ score matrix for seed and driver layout optimization. It will be created by run convert_deltaZ2_matrix.

n

row numbers.

m

colum number

use_popSize

Population size, GA::ga function parameter,default=50.

use_maxiter

Maximum iterations, GA::ga function parameter, default=100.

use_run

Early stopping criterion,GA::ga function parameter, default=50.

use_suggestions

Optional: initial solutions, GA::ga function parameter,default=NULL.

Examples

generate_matrix2<-function(n, m) {
    out_mat<-matrix(sample(1:10, 10 * n * 10 * m, replace = TRUE), nrow = 10 * n, ncol = 10 * m)
    rownames(out_mat)<-paste0("R_",1:dim(out_mat)[1])
    colnames(out_mat)<-paste0("C_",1:dim(out_mat)[2])
    return(out_mat)
}
base_matrix<-generate_matrix2(n=5,m=10)
out<-find_max_sum_submatrix(matrix=base_matrix, n=4, m=3)
#> Error in find_max_sum_submatrix(matrix = base_matrix, n = 4, m = 3): could not find function "find_max_sum_submatrix"
opt_mat<-out$submatrix
#> Error: object 'out' not found
if (FALSE) { # \dontrun{
} # }