R: Smooth gene expression, used primarily within...

smooth_count_matrix {sccore} | R Documentation

## Smooth gene expression, used primarily within conos::correctGenes. Used to smooth gene expression values in order to better represent the graph structure. Use diffusion of expression on graph with the equation dv = exp(-a * (v + b))

### Description

Smooth gene expression, used primarily within conos::correctGenes. Used to smooth gene expression values in order to better represent the graph structure. Use diffusion of expression on graph with the equation dv = exp(-a * (v + b))

### Usage

    smooth_count_matrix(
      edge_verts,
      edge_weights,
      count_matrix,
      is_label_fixed,
      max_n_iters = 10L,
      diffusion_fading = 1,
      diffusion_fading_const = 0.1,
      tol = 0.001,
      verbose = TRUE,
      normalize = FALSE
    )

### Arguments

`edge_verts` | edge vertices of igraph graph object
`edge_weights` | edge weights of igraph graph object
`count_matrix` | gene count matrix
`is_label_fixed` | boolean Whether label is fixed
`max_n_iters` | integer Maximal number of iterations (default=10)
`diffusion_fading` | numeric Constant used for diffusion on the graph, exp(-diffusion.fading * (edge_length + diffusion.fading.const)) (default=1.0)
`diffusion_fading_const` | numeric Another constant used for diffusion on the graph, exp(-diffusion.fading * (edge_length + diffusion.fading.const)) (default=0.1)
`tol` | numeric Absolute tolerance as a stopping criteria (default=1e-3)
`verbose` | boolean Verbose mode (default=TRUE)
`normalize` | boolean Whether to normalize values (default=FALSE)

### Value

matrix from input graph, with labels propagated

[Package sccore version 1.0.1 Index]