music_prop_bron: modified function of "music_prop" from MuSiC package using...

In CancanQi/BronchiCellPred: BronchiCellPred

Description

This function is to calculate the MuSiC deconvolution proportions

Usage

music_prop_bron(
  bulk.eset,
  sc.basis,
  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.basis	Gene signature matrix generated from bronchial biopsy scRNAseq data, using function music_basis from MuSiC package
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

CancanQi/BronchiCellPred documentation built on Dec. 17, 2021, 1:56 p.m.