MuSiC Deconvolution with Clusters

Source: R/utils.R

This function is to calculate the MuSiC deconvolution proportions with clusters

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.