music_prop.cluster: MuSiC Deconvolution with Clusters

In xuranw/MuSiC: Multi-subject single cell deconvolution

MuSiC Deconvolution with Clusters

Description

This function is to calculate the MuSiC deconvolution proportions with clusters

Usage

music_prop.cluster(
  bulk.mtx,
  sc.sce,
  group.markers,
  groups,
  clusters,
  samples,
  clusters.type,
  verbose = TRUE,
  iter.max = 1000,
  nu = 1e-04,
  eps = 0.01,
  centered = FALSE,
  normalize = FALSE,
  ...
)

Arguments

bulk.mtx	Matrix of expression for bulk data
sc.sce	SingleCellExperiment for single cell data
group.markers	list of gene names. The list include differential expressed genes within groups. List name must be the same as 'clusters.type'.
groups	character, the colData of single cell data used as groups;
clusters	character, the colData of single cell dataset used as clusters;
samples	character,the colData of single cell dataset used as samples;
clusters.type	list of cell types. The list identify groups of similar cell types.
verbose	logical, default as TRUE.
iter.max	numeric, maximum iteration number
nu	regulation parameter, take care of weight when taking reciprocal
eps	Threshold of convergence
centered	logic, subtract avg of Y and D
normalize	logic, divide Y and D by their standard deviation

Value

matrix of estimated proportions by MuSiC with cluster information.

See Also

music_basis; music_prop

xuranw/MuSiC documentation built on March 7, 2024, 11:45 a.m.