Remove extremely sparse columns

remove_sparse() removes columns from sparse and dense matrices that have a sparsity value greater than a user-defined threshold.

Usage

remove_sparse(x, threshold)

# S3 method for CsparseMatrix
remove_sparse(x, threshold)

# S3 method for matrix
remove_sparse(x, threshold)

Arguments

x

A matrix or CsparseMatrix.

threshold

A double between 0 and 1 specifying the sparsity threshold at which to remove columns.

Value

x with sparse columns removed.

Details

remove_sparse() is an S3 generic with methods for:

• CsparseMatrix

• matrix

Examples

# Create a sparse matrix with very sparse columns
x <- Matrix::rsparsematrix(10, 5, 0.1)
colnames(x) <- paste0("x", 1:5)
# Print x
x
#> 10 x 5 sparse Matrix of class "dgCMatrix"
#>        x1     x2   x3    x4 x5
#>  [1,] .    .      .    .     .
#>  [2,] .    .      .   -0.27  .
#>  [3,] .    .      .    .     .
#>  [4,] .    .      .    .     .
#>  [5,] .    .      .    .     .
#>  [6,] .    .      2.0  .     .
#>  [7,] 0.6  .      .    .     .
#>  [8,] .    .      .    .     .
#>  [9,] .   -0.064  .    .     .
#> [10,] .    .     -1.1  .     .

# Same matrix in dense format
xdense <- as.matrix(x)

# Drop duplicate columns
remove_sparse(x, threshold = 0.9)
#> 10 x 1 sparse Matrix of class "dgCMatrix"
#>         x3
#>  [1,]  .  
#>  [2,]  .  
#>  [3,]  .  
#>  [4,]  .  
#>  [5,]  .  
#>  [6,]  2.0
#>  [7,]  .  
#>  [8,]  .  
#>  [9,]  .  
#> [10,] -1.1
remove_sparse(xdense, threshold = 0.9)
#>         x3
#>  [1,]  0.0
#>  [2,]  0.0
#>  [3,]  0.0
#>  [4,]  0.0
#>  [5,]  0.0
#>  [6,]  2.0
#>  [7,]  0.0
#>  [8,]  0.0
#>  [9,]  0.0
#> [10,] -1.1