run_magic: Do the magic!

Usage Arguments

Usage

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run_magic(data, t_diffusion, lib_size_norm = TRUE, log_transform = FALSE,
  pseudo_count = 0.1, npca = 20, k = 30, ka = 10, epsilon = 1,
  rescale_percent = 0)

Arguments

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. epsilon = 0 is the uniform kernel.

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.


friedue/Rmagic documentation built on May 28, 2019, 8:40 p.m.