dot-smoothCms: .smoothCms

Description Usage Arguments Details Value See Also

Description

Performs weighted smoothening of cms scores

Usage

1
.smoothCms(knn, cms_raw, cell_names, k_min, k)

Arguments

knn

List with three elements. First "index" with indices of knn cells. Second "distance" with distances to knn cells. Third a slot named by group variable with group level of knn cells.

cms_raw

Matrix with raw cms scores for all cells specified in cell_names and knn. Colnames need to be "cms.

cell_names

Character vector with cell names corresponding to the rownames of the list elements in knn and rownames(cms_raw).

k_min

Numeric. Minimum number of knn to include. Default is NA (see Details).

k

Numeric. Number of k-nearest neighbours (knn) to use.

Details

Internal function to smooth cms scores. In a complete random setting cms scores are uniform distributed. To reduce the resulting random variance and enable visualization of local pattern cms scores can be smoothened assuming that within one region mixing is uniform. Generates smoothened cms scores using weigthed means of cms scores within the k-nearest neighbourhood. Reciprocal distances are used as weights.

Value

matrix with two columns ("cms_smooth", "cms").

See Also

.cmsCell, cms

Other helper functions: .cmsCell(), .defineSubspace(), .filterKnn(), .filterLocMin(), .ldfKnn()


almutlue/CellMixS documentation built on Dec. 22, 2020, 11:07 a.m.