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

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

Estimate cell type proportion with MuSiC and NNLS

Description

Estimate cell type proportion with MuSiC and NNLS

Usage

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

Arguments

Y	vector of bulk tissue expression
X	matrix, Signature matrix
S	vector of Avg. Library size
Sigma	matrix of Subject level variation (gene * cell type)
iter.max	numeric, maximum iteration number
nu	regulation parameter, take care of weight when taking recipical
eps	Thredshold 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

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