1 2 3 |
data |
the data in some format |
t_diffusion |
diffusion time; suggested to start with 6 and increase it up to 12. |
lib_size_norm |
Default: TRUE. |
log_transform |
Default: FALSE. |
npca |
number of PCA components that should be used; default: 20. |
k |
Number of nearest neighbors to use when running MAGIC. Default: 30. |
ka |
kNN-autotune parameter for running MAGIC; default: 10 |
epsilon |
a value for the standard deviation of the kernel. Default: 1.
|
rescale_percent |
To which percentile should the data be re-scaled. Note: Do not set this higher than 0 if you also want to log-transform. Default: 0. |
pseudo-count |
A number indicating how much should be added to avoid log-transformation of zeros. Default: 0.1. |
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