Description Usage Arguments Details Value
Specifies the droplets that are in the test set and debris set. The test set consists of droplets that will be classified by DIEM, the labels of which are allowed to change during the EM. The debris set consists of droplets with labels fixed to the debris group during the EM.
1 2 | set_debris_test_set(x, top_n = 10000, min_counts = 100,
min_genes = 100, fix_debris = NULL, verbose = FALSE)
|
x |
An SCE object. |
top_n |
A numeric value giving the total number of test droplets
and take the counts of the |
min_counts |
A numeric value that specifies the minimum total read/UMI counts a test droplet can have. |
min_genes |
A numeric value that specifies the minimum total genes detected a test droplet can have. |
fix_debris |
A character vector of droplet IDs that will be assigned to the debris set, regardless of its total counts or genes detected. |
verbose |
verbosity |
min_counts
and min_genes
specify the lower limit
that droplets in the test set must have. In addition,
the parameter top_n
specifies that at most the top top_n
should be included in the test set. The default is 10,000
in accordance with the typical maximum number of droplets
generated during a single-cell experiment, but should be changed
accordingly.
If the read/UMI count of the top_n
count-ranked droplet is greater
than min_counts
, then the min_counts
is
increased to this limit. The fix_debris
parameter allows
additional flexibility in specifying those droplets that are
included in the debris set. For example, it may be useful to
set droplets above a pre-determined MT
regardless of the total number of read/UMI counts present.
An SCE object.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.