music_prop: MuSiC Deconvolution

In nkoneill/mMuSiC: Deconvolution with Target and Reference Difference Extending MuSiC Version: 0.2.0

MuSiC Deconvolution

Description

This function is to calculate the MuSiC deconvolution proportions

Usage

music_prop(
  bulk.eset,
  sc.eset,
  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.eset	ExpressionSet for bulk data
sc.eset	ExpressionSet 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 phenoData of single cell dataset used as clusters;
samples	character,the phenoData 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 recipical
eps	Thredshold of convergence
centered	logic, substract 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

nkoneill/mMuSiC documentation built on Oct. 25, 2023, 2:39 a.m.