MuSiC Deconvolution

This function is to calculate the MuSiC deconvolution proportions

music_prop(
  bulk.mtx,
  sc.sce,
  markers = NULL,
  clusters,
  samples,
  select.ct = NULL,
  cell_size = NULL,
  ct.cov = FALSE,
  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

markers

vector or list of gene names, default as NULL. If NULL, use all genes that provided by both bulk and single cell dataset.

clusters

character, the colData of single cell dataset used as clusters;

samples

character,the colData of single cell dataset used as samples;

select.ct

vector of cell types, default as NULL. If NULL, then use all cell types provided by single cell dataset;

cell_size

data.frame of cell sizes. 1st column contains the names of cell types, 2nd column has the cell sizes per cell type. Default as NULL. If NULL, then estimate cell size from data;

ct.cov

logical. If TRUE, use the covariance across 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

a list with elements:

• Estimates of MuSiC;

• Estimates of NNLS;

• Weight of MuSiC;

• r.squared of MuSiC;

• Variance of MuSiC estimates.

See also

music_basis