music_prop: MuSiC Deconvolution

In xuranw/MuSiC: Multi-subject single cell deconvolution

MuSiC Deconvolution

Description

This function is to calculate the MuSiC deconvolution proportions

Usage

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

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