music.basic.ct: Estimate cell type proportion with MuSiC and NNLS

In xuranw/MuSiC: Multi-subject single cell deconvolution

Estimate cell type proportion with MuSiC and NNLS

Description

weight is estimated with cell type covariance

Usage

music.basic.ct(Y, X, S, Sigma.ct, iter.max, nu, eps)

Arguments

Y	vector of bulk tissue expression
X	matrix, Signature matrix
S	vector of Avg. Library size
Sigma.ct	matrix of Subject level variation with
iter.max	numeric, maximum iteration number
nu	regulation parameter, take care of weight when taking reciprocal
eps	Threshold of convergence

Value

a list with elements:

• p.nnls: vector of cell type proportions estimated by nnls (add up to 1);

• q.nnls: vector of original estimation from nnls;

• fit.nnls: fitted value of Y from nnls;

• resid.nnls: residual value from nnls;

• p.weight: vector of cell type proportions estimated by weighted-nnls (add up to 1);

• q.weight: vector of original estimation from weight-nnls;

• fit.weight: fitted value of Y from weighted-nnls;

• resid.weight: residual value from weighted-nnls;

• weight.gene: weight calculated from weighted-nnls;

• converge: 'Reach Maxiter', 'Converge at m';

• rsd: residual value from weighted-nnls transfromed by weight;

• R.squared: R square of weighted-nnls:

• var.p: variance of weighted-nnls estimated cell type proportions.

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