Read expression matrix

Function to read an expression matrix into a sparse matrix.

Usage

readExprMatrix(
  path,
  cores = determine_cores(),
  transpose = FALSE,
  feat_type = "rna",
  expression_matrix_class = c("dgCMatrix", "DelayedArray"),
  ...
)

Arguments

path

path to the expression matrix

cores

number of cores to use

transpose

transpose matrix

feat_type

feature type (e.g. "rna", "dna", "protein")

expression_matrix_class

class of expression matrix to use (e.g. 'dgCMatrix', 'DelayedArray')

...

additional params to pass

Value

sparse matrix

Details

The expression matrix needs to have both unique column names and row names

Examples

x <- matrix(seq_len(100), nrow = 10)
temporal_dir <- tempdir()
write.csv(x, paste0(temporal_dir, "/mymatrix.csv"))

readExprMatrix(paste0(temporal_dir, "/mymatrix.csv"))
#> 10 x 10 sparse Matrix of class "dgCMatrix"
#>   [[ suppressing 10 column names ‘V1’, ‘V2’, ‘V3’ ... ]]
#>                                  
#> 1   1 11 21 31 41 51 61 71 81  91
#> 2   2 12 22 32 42 52 62 72 82  92
#> 3   3 13 23 33 43 53 63 73 83  93
#> 4   4 14 24 34 44 54 64 74 84  94
#> 5   5 15 25 35 45 55 65 75 85  95
#> 6   6 16 26 36 46 56 66 76 86  96
#> 7   7 17 27 37 47 57 67 77 87  97
#> 8   8 18 28 38 48 58 68 78 88  98
#> 9   9 19 29 39 49 59 69 79 89  99
#> 10 10 20 30 40 50 60 70 80 90 100