Downsample each cell to a specified number of UMIs. Includes an option to upsample cells below specified UMI as well.
SampleUMI(data, max.umi = 1000, upsample = FALSE, verbose = FALSE)Matrix with the raw count data
Number of UMIs to sample to
Upsamples all cells with fewer than max.umi
Display the progress bar
Matrix with downsampled data
data("pbmc_small")
counts = as.matrix(x = GetAssayData(object = pbmc_small, assay = "RNA", slot = "counts"))
downsampled = SampleUMI(data = counts)
head(x = downsampled)
#> 6 x 80 sparse Matrix of class "dgCMatrix"
#> [[ suppressing 80 column names ‘ATGCCAGAACGACT’, ‘CATGGCCTGTGCAT’, ‘GAACCTGATGAACC’ ... ]]
#>
#> MS4A1 . . . . . . . . . . 2 2 4 4 2 3 3 4 2 3 . . . . 1 . . . . .
#> CD79B 1 . . . . . . . . 1 2 4 3 3 2 3 1 2 2 5 . . . . . . . . . 1
#> CD79A . . . . . . . . . . . 5 2 2 5 8 1 5 5 12 . . 1 . . . . 1 . .
#> HLA-DRA . 1 . . 1 1 . 1 . . 14 28 18 7 15 28 7 26 10 16 7 22 . 10 6 . 4 3 7 13
#> TCL1A . . . . . . . . . . 3 . 2 4 . . 3 3 3 2 . . . . . . . . . .
#> HLA-DQB1 1 . . . . . . . . . 1 6 2 2 2 8 2 2 1 2 . 3 . . . . 1 . 1 .
#>
#> MS4A1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> CD79B 1 . 2 . . . . . . . . . . . . . . . . . 1 . 1 1 2 2 . . 3 . .
#> CD79A . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> HLA-DRA . 1 . . 1 . 1 1 . . . . . . . 1 1 1 . . 10 10 4 1 6 28 10 13 5 8 108
#> TCL1A . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
#> HLA-DQB1 . . . . . . . . . . . . . . . . . . . . . 1 1 . 2 . . 1 1 . 21
#>
#> MS4A1 . . . . . . 1 . . . . . . . . . . . .
#> CD79B . . 4 1 . . . . . . . . . . . . . . .
#> CD79A . . 8 . . . . 1 . . . . . . . . . . .
#> HLA-DRA 93 41 42 138 77 76 15 19 104 1 . . . 2 1 1 . 2 7
#> TCL1A . . 4 . . . . . . . . . . . . . . . .
#> HLA-DQB1 21 3 5 11 11 10 1 2 11 . . . . . . . . . 1