Create a dbSparseMatrix or dbDenseMatrix object

Create an S4 dbMatrix object in sparse or dense triplet vector format.

Usage

dbMatrix(
  value,
  class = NULL,
  con = NULL,
  overwrite = FALSE,
  name = "dbMatrix",
  dims = NULL,
  dim_names = NULL,
  mtx_rowname_file_path,
  mtx_rowname_col_idx = 1,
  mtx_colname_file_path,
  mtx_colname_col_idx = 1,
  ...
)

Arguments

value

data to be added to the database. See details for supported data types (required)

class

class of the dbMatrix: dbDenseMatrix or dbSparseMatrix (required)

con

DBI or duckdb connection object (required)

overwrite

whether to overwrite if table already exists in database (required)

name

table name to assign within database (required, default: "dbMatrix")

dims

dimensions of the matrix (optional: [int, int])

dim_names

dimension names of the matrix (optional: list(enum, enum))

mtx_rowname_file_path

path to .mtx rowname file to be read into (optional) database. by default, no header is assumed.

mtx_rowname_col_idx

column index of row name file (optional)

mtx_colname_file_path

path to .mtx colname file to be read into database. by default, no header is assumed. (optional)

mtx_colname_col_idx

column index of column name file (optional)

...

additional params to pass

Details

This function reads in data into a pre-existing DuckDB database. Supported value data types:

• dgCMatrix In-memory sparse matrix from the Matrix package

• dgTMatrix In-memory triplet vector or COO matrix

• matrix In-memory dense matrix from base R

• .mtx Path to .mtx file

• .csv Path to .csv file

• tbl_duckdb_connection Table in DuckDB database in ijx format from existing dbMatrix object. dims and dim_names must be specified if value is tbl_duckdb_connection.

Examples

dgc = readRDS(system.file("data", "dgc.rds", package = "dbMatrix"))
#> Loading required package: Matrix
con <- DBI::dbConnect(duckdb::duckdb(), ":memory:")
dbSparse <- dbMatrix(
  value = dgc,
  con = con,
  name = "sparse_matrix",
  class = "dbSparseMatrix",
  overwrite = TRUE
)
dbSparse
#> 634 x 624  matrix of class "dbSparseMatrix"
#> [[ Colnames 'AAAGGGATGTAGCAAG-1', 'AAATGGCATGTCTTGT-1', 'AAATGGTCAATGTGCC-1' ... suppressing 618 ...'TTGTCGTTCAGTTACC-1', 'TTGTGGCCCTGACAGT-1', 'TTGTTCAGTGTGCTAC-1' ]]
#>                                  
#> Gna12         1 2 1 1 9 1 3 5 3 .
#> Ccnd2         . 1 1 . . 1 . 1 1 .
#> Btbd17        . 1 1 1 . . 2 . . .
#> 
#> ......suppressing 614 columns and 628 rows
#> 
#> Gm19935       . 1 . . . . . . . .
#> 9630013A20Rik . . . . . . . . . .
#> 2900040C04Rik 1 . . . . . . . . 1